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49 results on '"Kassemeyer S"'

1. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Author

Nass, Karol, Redecke, Lars, Perbandt, M, Yefanov, O, Klinge, M, Koopmann, R, Stellato, F, Gabdulkhakov, A, Schönherr, R, Rehders, D, Lahey-Rudolph, JM, Aquila, A, Barty, A, Basu, S, Doak, RB, Duden, R, Frank, M, Fromme, R, Kassemeyer, S, Katona, G, Kirian, R, Liu, H, Majoul, I, Martin-Garcia, JM, Messerschmidt, M, Shoeman, RL, Weierstall, U, Westenhoff, S, White, TA, Williams, GJ, Yoon, CH, Zatsepin, N, Fromme, P, Duszenko, M, Chapman, HN, and Betzel, C

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Rare Diseases, Infectious Diseases, Vector-Borne Diseases, Infection, Good Health and Well Being, Amino Acid Sequence, Animals, Binding Sites, Catalytic Domain, Cloning, Molecular, Coenzymes, Crystallization, Guanosine Monophosphate, IMP Dehydrogenase, Models, Molecular, Protein Conformation, Sf9 Cells, Trypanosoma brucei brucei
Abstract

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

Published
2020

2. Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

Author

Loh, N. D., Hampton, C. Y., Martin, A. V., Starodub, D., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Lomb, L., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. M., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R. N. C., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S. P., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Bucksbaum, P., Hodgson, K. O., Strüder, L., Ullrich, J., Frank, M., Schlichting, I., Chapman, H. N., and Bogan, M. J.

Published
2012
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3. Corrigendum: Diffraction data of core-shell nanoparticles from an X-ray free electron laser

Author

Li, X., Chiu, C., Wang, H., Kassemeyer, S., Botha, S., Shoeman, R., Lawrence, R., Kupitz, C., Kirian, R., James, D., Wang, D., Nelson, G., Messerschmidt, M., Boutet, S., Williams, G., Hartmann, E., Jafarpour, A., Foucar, L., Barty, A., Chapman, H., Liang, M., Menzel, A., Wang, F., Basu, S., Fromme, R., Doak, B., Fromme, P., Weierstall, U., Huang, M., Spence, J., Schlichting, I., Hogue, B., and Liu, H.

Published
2017

4. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Author

Ekeberg, T, Svenda, M, Seibert, MM, Abergel, C, Maia, FRNC, Seltzer, V, DePonte, DP, Aquila, A, Andreasson, J, Iwan, B, Jonsson, O, Westphal, D, Odic, D, Andersson, I, Barty, A, Liang, M, Martin, AV, Gumprecht, L, Fleckenstein, H, Bajt, S, Barthelmess, M, Coppola, N, Claverie, J-M, Loh, ND, Bostedt, C, Bozek, JD, Krzywinski, J, Messerschmidt, M, Bogan, MJ, Hampton, CY, Sierra, RG, Frank, M, Shoeman, RL, Lomb, L, Foucar, L, Epp, SW, Rolles, D, Rudenko, A, Hartmann, R, Hartmann, A, Kimmel, N, Holl, P, Weidenspointner, G, Rudek, B, Erk, B, Kassemeyer, S, Schlichting, I, Strueder, L, Ullrich, J, Schmidt, C, Krasniqi, F, Hauser, G, Reich, C, Soltau, H, Schorb, S, Hirsemann, H, Wunderer, C, Graafsma, H, Chapman, H, Hajdu, J, Ekeberg, T, Svenda, M, Seibert, MM, Abergel, C, Maia, FRNC, Seltzer, V, DePonte, DP, Aquila, A, Andreasson, J, Iwan, B, Jonsson, O, Westphal, D, Odic, D, Andersson, I, Barty, A, Liang, M, Martin, AV, Gumprecht, L, Fleckenstein, H, Bajt, S, Barthelmess, M, Coppola, N, Claverie, J-M, Loh, ND, Bostedt, C, Bozek, JD, Krzywinski, J, Messerschmidt, M, Bogan, MJ, Hampton, CY, Sierra, RG, Frank, M, Shoeman, RL, Lomb, L, Foucar, L, Epp, SW, Rolles, D, Rudenko, A, Hartmann, R, Hartmann, A, Kimmel, N, Holl, P, Weidenspointner, G, Rudek, B, Erk, B, Kassemeyer, S, Schlichting, I, Strueder, L, Ullrich, J, Schmidt, C, Krasniqi, F, Hauser, G, Reich, C, Soltau, H, Schorb, S, Hirsemann, H, Wunderer, C, Graafsma, H, Chapman, H, and Hajdu, J

Abstract

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

Published
2016

5. Native inhibition of Trypanosoma brucei cathepsin B revealed by an X-ray laser at 2.1 \u01fa resolution

Author

Redecke L, Nass K, DePonte DP, White TA, Rehders D, Barty A, Stellato F, Liang M, Barends TRM, Boutet S, Williams GJ, Messerschmidt M, Seibert MM, Aquila A, Arnlund D, Bajt S, Barth T, Bogan MJ, Caleman C, Chao T, Doak RB, Fleckenstein H, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Johansson LC, Kassemeyer S, Katona G, Kirian R, Koopmann R, Kupitz C, Lomb L, Martin AV, Mogk S, Neutze R, Shoeman RL, Steinbrener J, Timneanu N, Wang D, Weierstall U, Zatsepin NA, Spence JCH, Fromme P, and Schlichting I

Published
2013

6. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

Author

Barty, A, Caleman, C, Aquila, A, Timneanu, N, Lomb, L, White, TA, Andreasson, J, Arnlund, D, Bajt, S, Barends, TRM, Barthelmess, M, Bogan, MJ, Bostedt, C, Bozek, JD, Coffee, R, Coppola, N, Davidsson, J, DePonte, DP, Doak, RB, Ekeberg, T, Elser, V, Epp, SW, Erk, B, Fleckenstein, H, Foucar, L, Fromme, P, Graafsma, H, Gumprecht, L, Hajdu, J, Hampton, CY, Hartmann, R, Hartmann, A, Hauser, G, Hirsemann, H, Holl, P, Hunter, MS, Johansson, L, Kassemeyer, S, Kimmel, N, and Kirian

Published
2012

7. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

Author

Boutet S, Lomb L, Williams GJ, Barends TRM, Aquila A, Doak RB, Weierstall U, DePonte DP, Steinbrener J, Shoeman RL, Messerschmidt M, Barty A, White TA, Kassemeyer S, Kirian RA, Seibert MM, Montanez PA, Kenney C, Herbst R, Hart P, Pines J, Haller G, Gruner SM, Philipp HT, Tate MW, Hromalik M, Koerner LJ, van Bakel N, Morse J, Ghonsalves W, Arnlund D, Bogan MJ, Caleman C, Fromme R, Hampton CY, Hunter MS, Johansson LC, Katona G, Kupitz C, Liang MN, Martin AV, Nass K, Redecke L, Stellato F, Timneanu N, and Wang DJ

Published
2012

8. Radiation Damage in Protein Serial Femtosecond Crystallography using an X-ray Free-electron Laser

Author

Lomb L, Barends TRM, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L, Hartmann R, Rudek B, Rolles D, Rudenko A, Shoeman RL, Andreasson J, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, DePonte DP, Doak RB, Ekeberg T, Fleckenstein H, Fromme P, Gebhardt M, Graafsma H, Gumprecht L, Hampton CY, Hartmann A, Hauser G, Hirsemann H, Holl P, Holton JM, Hunter MS, Kabsch W, Kimmel N, Kirian RA, Liang M, Maia FRNC, Meinhart A, Marchesini S, Martin AV, Nass K, and Reich C

Published
2011

9. Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)

Author

Kupitz, C., primary, Basu, S., additional, Grotjohann, I., additional, Fromme, R., additional, Zatsepin, N., additional, Rendek, K.N., additional, Hunter, M., additional, Shoeman, R.L., additional, White, T.A., additional, Wang, D., additional, James, D., additional, Yang, J.-H., additional, Cobb, D.E., additional, Reeder, B., additional, Sierra, R.G., additional, Liu, H., additional, Barty, A., additional, Aquila, A., additional, Deponte, D., additional, Kirian, R., additional, Bari, S., additional, Bergkamp, J.J., additional, Beyerlein, K., additional, Bogan, M.J., additional, Caleman, C., additional, Chao, T.-C., additional, Conrad, C.E., additional, Davis, K.M., additional, Fleckenstein, H., additional, Galli, L., additional, Hau-Riege, S.P., additional, Kassemeyer, S., additional, Laksmono, H., additional, Liang, M., additional, Lomb, L., additional, Marchesini, S., additional, Martin, A.V., additional, Messerschmidt, M., additional, Milathianaki, D., additional, Nass, K., additional, Ros, A., additional, Roy-Chowdhury, S., additional, Schmidt, K., additional, Seibert, M., additional, Steinbrener, J., additional, Stellato, F., additional, Yan, L., additional, Yoon, C., additional, Moore, T.A., additional, Moore, A.L., additional, Pushkar, Y., additional, Williams, G.J., additional, Boutet, S., additional, Doak, R.B., additional, Weierstall, U., additional, Frank, M., additional, Chapman, H.N., additional, Spence, J.C.H., additional, and Fromme, P., additional

Published
2015
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10. Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S state after two flashes(S3)

Author

Kupitz, C., primary, Basu, S., additional, Grotjohann, I., additional, Fromme, R., additional, Zatsepin, N., additional, Rendek, K.N., additional, Hunter, M., additional, Shoeman, R.L., additional, White, T.A., additional, Wang, D., additional, James, D., additional, Yang, J.H., additional, Cobb, D.E., additional, Reeder, B., additional, Sierra, R.G., additional, Liu, H., additional, Barty, A., additional, Aquila, A., additional, Deponte, D., additional, Kirian, R.A., additional, Bari, S., additional, Bergkamp, J.J., additional, Beyerlein, K., additional, Bogan, M.J., additional, Caleman, C., additional, Chao, T.C., additional, Conrad, C.E., additional, Davis, K.M., additional, Fleckenstein, H., additional, Galli, L., additional, Hau-Riege, S.P., additional, Kassemeyer, S., additional, Laksmono, H., additional, Liang, M., additional, Lomb, L., additional, Marchesini, S., additional, Martin, A.V., additional, Messerschmidt, M., additional, Milathianaki, D., additional, Nass, K., additional, Ros, A., additional, Roy-Chowdhury, S., additional, Schmidt, K., additional, Seibert, M., additional, Steinbrener, J., additional, Stellato, F., additional, Yan, L., additional, Yoon, C., additional, Moore, T.A., additional, Moore, A.L., additional, Pushkar, Y., additional, Williams, G.J., additional, and Boutet, S., additional

Published
2014
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11. Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state

Author

Kupitz, C., primary, Basu, S., additional, Grotjohann, I., additional, Fromme, R., additional, Zatsepin, N., additional, Rendek, K.N., additional, Hunter, M., additional, Shoeman, R.L., additional, White, T.A., additional, Wang, D., additional, James, D., additional, Yang, J.H., additional, Cobb, D.E., additional, Reeder, B., additional, Sierra, R.G., additional, Liu, H., additional, Barty, A., additional, Aquila, A., additional, Deponte, D., additional, Kirian, R.A., additional, Bari, S., additional, Bergkamp, J.J., additional, Beyerlein, K., additional, Bogan, M.J., additional, Caleman, C., additional, Chao, T.-C., additional, Conrad, C.E., additional, Davis, K.M., additional, Fleckenstein, H., additional, Galli, L., additional, Hau-Riege, S.P., additional, Kassemeyer, S., additional, Laksmono, H., additional, Liang, M., additional, Lomb, L., additional, Marchesini, S., additional, Martin, A.V., additional, Messerschmidt, M., additional, Milathianaki, D., additional, Nass, K., additional, Ros, A., additional, Roy-Chowdhury, S., additional, Schmidt, K., additional, Seibert, M., additional, Steinbrener, J., additional, Stellato, F., additional, Yan, L., additional, Yoon, C., additional, Moore, T.A., additional, Moore, A.L., additional, Pushkar, Y., additional, Williams, G.J., additional, Boutet, S., additional, Doak, R.B., additional, Weierstall, U., additional, Frank, M., additional, Chapman, H.N., additional, Spence, J.C.H., additional, and Fromme, P., additional

Published
2014
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12. Mesoscale morphology of airborne core-shell nanoparticle clusters : x-ray laser coherent diffraction imaging

Author

Pedersoli, E., Loh, N. D., Capotondi, F., Hampton, C. Y., Sierra, R. G., Starodub, D., Bostedt, C., Bozek, J., Nelson, A. J., Aslam, M., Li, S., Dravid, V. P., Martin, A. V., Aquila, A., Barty, A., Fleckenstein, H., Gumprecht, L., Liang, M., Nass, K., Schulz, J., White, T. A., Coppola, N., Bajt, S., Barthelmess, M., Graafsma, H., Hirsemann, H., Wunderer, C., Epp, S. W., Erk, B., Rudek, B., Rudenko, A., Foucar, L., Kassemeyer, S., Lomb, L., Rolles, D., Shoeman, R. L., Steinbrener, J., Hartmann, R., Hartmann, A., Hauser, G., Holl, P., Kimmel, N., Reich, C., Soltau, H., Weidenspointner, G., Benner, W. H., Farquar, G. R., Hau-Riege, S. P., Hunter, M. S., Ekeberg, Tomas, Hantke, Max, Maia, Filipe R. N. C., Tobias, H. J., Marchesini, S., Frank, M., Strueder, L., Schlichting, I., Ullrich, J., Chapman, H. N., Bucksbaum, P. H., Kiskinova, M., Bogan, M. J., Pedersoli, E., Loh, N. D., Capotondi, F., Hampton, C. Y., Sierra, R. G., Starodub, D., Bostedt, C., Bozek, J., Nelson, A. J., Aslam, M., Li, S., Dravid, V. P., Martin, A. V., Aquila, A., Barty, A., Fleckenstein, H., Gumprecht, L., Liang, M., Nass, K., Schulz, J., White, T. A., Coppola, N., Bajt, S., Barthelmess, M., Graafsma, H., Hirsemann, H., Wunderer, C., Epp, S. W., Erk, B., Rudek, B., Rudenko, A., Foucar, L., Kassemeyer, S., Lomb, L., Rolles, D., Shoeman, R. L., Steinbrener, J., Hartmann, R., Hartmann, A., Hauser, G., Holl, P., Kimmel, N., Reich, C., Soltau, H., Weidenspointner, G., Benner, W. H., Farquar, G. R., Hau-Riege, S. P., Hunter, M. S., Ekeberg, Tomas, Hantke, Max, Maia, Filipe R. N. C., Tobias, H. J., Marchesini, S., Frank, M., Strueder, L., Schlichting, I., Ullrich, J., Chapman, H. N., Bucksbaum, P. H., Kiskinova, M., and Bogan, M. J.

Abstract

Unraveling the complex morphology of functional materials like core-shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core-shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with similar to 10 nm core diameter and similar to 30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core-shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.

Published
2013
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13. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

Author

Johansson, LC, Arnlund, D, Katona, G, White, TA, Barty, A, DePonte, DP, Shoeman, RL, Wickstrand, C, Sharma, A, Williams, GJ, Aquila, A, Bogan, MJ, Caleman, C, Davidsson, J, Doak, RB, Frank, M, Fromme, R, Galli, L, Grotjohann, I, Hunter, MS, Kassemeyer, S, Kirian, RA, Kupitz, C, Liang, M, Lomb, L, Malmerberg, E, Martin, AV, Messerschmidt, M, Nass, K, Redecke, L, Seibert, MM, Sjoehamn, J, Steinbrener, J, Stellato, F, Wang, D, Wahlgren, WY, Weierstall, U, Westenhoff, S, Zatsepin, NA, Boutet, S, Spence, JCH, Schlichting, I, Chapman, HN, Fromme, P, Neutze, R, Johansson, LC, Arnlund, D, Katona, G, White, TA, Barty, A, DePonte, DP, Shoeman, RL, Wickstrand, C, Sharma, A, Williams, GJ, Aquila, A, Bogan, MJ, Caleman, C, Davidsson, J, Doak, RB, Frank, M, Fromme, R, Galli, L, Grotjohann, I, Hunter, MS, Kassemeyer, S, Kirian, RA, Kupitz, C, Liang, M, Lomb, L, Malmerberg, E, Martin, AV, Messerschmidt, M, Nass, K, Redecke, L, Seibert, MM, Sjoehamn, J, Steinbrener, J, Stellato, F, Wang, D, Wahlgren, WY, Weierstall, U, Westenhoff, S, Zatsepin, NA, Boutet, S, Spence, JCH, Schlichting, I, Chapman, HN, Fromme, P, and Neutze, R

Abstract

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

Published
2013

14. Noise-robust coherent diffractive imaging with a single diffraction pattern

Author

Martin, A. V., Wang, F., Loh, N. D., Ekeberg, Tomas, Maia, F. R. N. C., Hantke, Max Felix, van der Schot, Gijs, Hampton, C. Y., Sierra, R. G., Aquila, A., Bajt, S., Barthelmess, M., Bostedt, C., Bozek, J. D., Coppola, N., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Liang, M., Lomb, L., Marchesini, S., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strueder, L., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C. B., Barty, A., Schlichting, I., Bogan, M. J., Chapman, H. N., Martin, A. V., Wang, F., Loh, N. D., Ekeberg, Tomas, Maia, F. R. N. C., Hantke, Max Felix, van der Schot, Gijs, Hampton, C. Y., Sierra, R. G., Aquila, A., Bajt, S., Barthelmess, M., Bostedt, C., Bozek, J. D., Coppola, N., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Liang, M., Lomb, L., Marchesini, S., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strueder, L., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C. B., Barty, A., Schlichting, I., Bogan, M. J., and Chapman, H. N.

Abstract

The resolution of single-shot coherent diffractive imaging at X-ray free-electron laser facilities is limited by the low signal-to-noise level of diffraction data at high scattering angles. The iterative reconstruction methods, which phase a continuous diffraction pattern to produce an image, must be able to extract information from these weak signals to obtain the best quality images. Here we show how to modify iterative reconstruction methods to improve tolerance to noise. The method is demonstrated with the hybrid input-output method on both simulated data and single-shot diffraction patterns taken at the Linac Coherent Light Source. (C) 2012 Optical Society of America

Published
2012

15. Femtosecond dark-field imaging with an X-ray free electron laser

Author

Martin, A. V., Loh, N. D., Hampton, C. Y., Sierra, R. G., Wang, F., Aquila, A., Bajt, S., Barthelmess, M., Bostedt, C., Bozek, J. D., Coppola, N., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Liang, M., Lomb, L., Maia, F. R. N. C., Marchesini, S., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strüder, L., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C. B., Barty, A., Schlichting, I., Bogan, M. J., Chapman, H. N., Martin, A. V., Loh, N. D., Hampton, C. Y., Sierra, R. G., Wang, F., Aquila, A., Bajt, S., Barthelmess, M., Bostedt, C., Bozek, J. D., Coppola, N., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Liang, M., Lomb, L., Maia, F. R. N. C., Marchesini, S., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strüder, L., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C. B., Barty, A., Schlichting, I., Bogan, M. J., and Chapman, H. N.

Abstract

The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.

Published
2012
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16. Profiling structured beams using injected aerosols

Author

Duane Loh, N., Starodub, D., Lomb, L., Hampton, C. Y., Martin, A. V., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. S., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R. N. C., Ekeberg, T., Hantke, Max Felix, Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Henry Benner, W., Hau-Riege, S., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Strueder, L., Ullrich, J., Bucksbaum, P., Hodgson, K. O., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J., Duane Loh, N., Starodub, D., Lomb, L., Hampton, C. Y., Martin, A. V., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. S., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R. N. C., Ekeberg, T., Hantke, Max Felix, Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Henry Benner, W., Hau-Riege, S., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Strueder, L., Ullrich, J., Bucksbaum, P., Hodgson, K. O., Frank, M., Schlichting, I., Chapman, H. N., and Bogan, M. J.

Abstract

Profiling structured beams produced by X-ray free-electron lasers (FELs) is crucial to both maximizing signal intensity for weakly scattering targets and interpreting their scattering patterns. Earlier ablative imprint studies describe how to infer the X-ray beam profile from the damage that an attenuated beam inflicts on a substrate. However, the beams in-situ profile is not directly accessible with imprint studies because the damage profile could be different from the actual beam profile. On the other hand, although a Shack-Hartmann sensor is capable of in-situ profiling, its lenses may be quickly damaged at the intense focus of hard X-ray FEL beams. We describe a new approach that probes the in-situ morphology of the intense FEL focus. By studying the translations in diffraction patterns from an ensemble of randomly injected sub-micron latex spheres, we were able to determine the non-Gaussian nature of the intense FEL beam at the Linac Coherent Light Source (SLAC National Laboratory) near the FEL focus. We discuss an experimental application of such a beam-profiling technique, and the limitations we need to overcome before it can be widely applied.

Published
2012
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17. Time-resolved protein nanocrystallography using an X-ray free-electron laser

Author

Aquila, A, Hunter, MS, Doak, RB, Kirian, RA, Fromme, P, White, TA, Andreasson, J, Arnlund, D, Bajt, S, Barends, TRM, Barthelmess, M, Bogan, MJ, Bostedt, C, Bottin, H, Bozek, JD, Caleman, C, Coppola, N, Davidsson, J, DePonte, DP, Elser, V, Epp, SW, Erk, B, Fleckenstein, H, Foucar, L, Frank, M, Fromme, R, Graafsma, H, Grotjohann, I, Gumprecht, L, Hajdu, J, Hampton, CY, Hartmann, A, Hartmann, R, Hauriege, S, Hauser, G, Hirsemann, H, Holl, P, Holton, JM, Hoemke, A, Johansson, L, Kimmel, N, Kassemeyer, S, Krasniqi, F, Kuehnel, K, Liang, M, Lomb, L, Malmerberg, E, Marchesini, S, Martin, AV, Maia, FRNC, Messerschmidt, M, Nass, K, Reich, C, Neutze, R, Rolles, D, Rudek, B, Rudenko, A, Schlichting, I, Schmidt, C, Schmidt, KE, Schulz, J, Seibert, MM, Shoeman, RL, Sierra, R, Soltau, H, Starodub, D, Stellato, F, Stern, S, Strueder, L, Timneanu, N, Ullrich, J, Wang, X, Williams, GJ, Weidenspointner, G, Weierstall, U, Wunderer, C, Barty, A, Spence, JCH, Chapman, HN, Aquila, A, Hunter, MS, Doak, RB, Kirian, RA, Fromme, P, White, TA, Andreasson, J, Arnlund, D, Bajt, S, Barends, TRM, Barthelmess, M, Bogan, MJ, Bostedt, C, Bottin, H, Bozek, JD, Caleman, C, Coppola, N, Davidsson, J, DePonte, DP, Elser, V, Epp, SW, Erk, B, Fleckenstein, H, Foucar, L, Frank, M, Fromme, R, Graafsma, H, Grotjohann, I, Gumprecht, L, Hajdu, J, Hampton, CY, Hartmann, A, Hartmann, R, Hauriege, S, Hauser, G, Hirsemann, H, Holl, P, Holton, JM, Hoemke, A, Johansson, L, Kimmel, N, Kassemeyer, S, Krasniqi, F, Kuehnel, K, Liang, M, Lomb, L, Malmerberg, E, Marchesini, S, Martin, AV, Maia, FRNC, Messerschmidt, M, Nass, K, Reich, C, Neutze, R, Rolles, D, Rudek, B, Rudenko, A, Schlichting, I, Schmidt, C, Schmidt, KE, Schulz, J, Seibert, MM, Shoeman, RL, Sierra, R, Soltau, H, Starodub, D, Stellato, F, Stern, S, Strueder, L, Timneanu, N, Ullrich, J, Wang, X, Williams, GJ, Weidenspointner, G, Weierstall, U, Wunderer, C, Barty, A, Spence, JCH, and Chapman, HN

Abstract

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

Published
2012

18. Serial femtosecond crystallography structure of a photosynthetic reaction center

Author

Johansson, L.C., primary, Arnlund, D., additional, Katona, G., additional, White, T.A., additional, Barty, A., additional, DePonte, D.P., additional, Shoeman, R.L., additional, Wickstrand, C., additional, Sharma, A., additional, Williams, G.J., additional, Aquila, A., additional, Bogan, M.J., additional, Caleman, C., additional, Davidsson, J., additional, Doak, R.B., additional, Frank, M., additional, Fromme, R., additional, Galli, L., additional, Grotjohann, I., additional, Hunter, M.S., additional, Kassemeyer, S., additional, Kirian, R.A., additional, Kupitz, C., additional, Liang, M., additional, Lomb, L., additional, Malmerberg, E., additional, Martin, A.V., additional, Messerschmidt, M., additional, Nass, K., additional, Redecke, L., additional, Seibert, M.M., additional, Sjohamn, J., additional, Steinbrener, J., additional, Stellato, F., additional, Wang, D., additional, Wahlgren, W.Y., additional, Weierstall, U., additional, Westenhoff, S., additional, Zatsepin, N.A., additional, Boutet, S., additional, Spence, J.C.H., additional, Schlichting, I., additional, Chapman, H.N., additional, Fromme, P., additional, and Neutze, R., additional

Published
2013
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19. Mesoscale morphology of airborne core–shell nanoparticle clusters: x-ray laser coherent diffraction imaging

Author

Pedersoli, E, primary, Loh, N D, additional, Capotondi, F, additional, Hampton, C Y, additional, Sierra, R G, additional, Starodub, D, additional, Bostedt, C, additional, Bozek, J, additional, Nelson, A J, additional, Aslam, M, additional, Li, S, additional, Dravid, V P, additional, Martin, A V, additional, Aquila, A, additional, Barty, A, additional, Fleckenstein, H, additional, Gumprecht, L, additional, Liang, M, additional, Nass, K, additional, Schulz, J, additional, White, T A, additional, Coppola, N, additional, Bajt, S, additional, Barthelmess, M, additional, Graafsma, H, additional, Hirsemann, H, additional, Wunderer, C, additional, Epp, S W, additional, Erk, B, additional, Rudek, B, additional, Rudenko, A, additional, Foucar, L, additional, Kassemeyer, S, additional, Lomb, L, additional, Rolles, D, additional, Shoeman, R L, additional, Steinbrener, J, additional, Hartmann, R, additional, Hartmann, A, additional, Hauser, G, additional, Holl, P, additional, Kimmel, N, additional, Reich, C, additional, Soltau, H, additional, Weidenspointner, G, additional, Benner, W H, additional, Farquar, G R, additional, Hau-Riege, S P, additional, Hunter, M S, additional, Ekeberg, T, additional, Hantke, M, additional, Maia, F R N C, additional, Tobias, H J, additional, Marchesini, S, additional, Frank, M, additional, Strüder, L, additional, Schlichting, I, additional, Ullrich, J, additional, Chapman, H N, additional, Bucksbaum, P H, additional, Kiskinova, M, additional, and Bogan, M J, additional

Published
2013
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20. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns

Author

Starodub, D., primary, Aquila, A., additional, Bajt, S., additional, Barthelmess, M., additional, Barty, A., additional, Bostedt, C., additional, Bozek, J.D., additional, Coppola, N., additional, Doak, R.B., additional, Epp, S.W., additional, Erk, B., additional, Foucar, L., additional, Gumprecht, L., additional, Hampton, C.Y., additional, Hartmann, A., additional, Hartmann, R., additional, Holl, P., additional, Kassemeyer, S., additional, Kimmel, N., additional, Laksmono, H., additional, Liang, M., additional, Loh, N.D., additional, Lomb, L., additional, Martin, A.V., additional, Nass, K., additional, Reich, C., additional, Rolles, D., additional, Rudek, B., additional, Rudenko, A., additional, Schulz, J., additional, Shoeman, R.L., additional, Sierra, R.G., additional, Soltau, H., additional, Steinbrener, J., additional, Stellato, F., additional, Stern, S., additional, Weidenspointner, G., additional, Frank, M., additional, Ullrich, J., additional, Strüder, L., additional, Schlichting, I., additional, Chapman, H.N., additional, Spence, J.C.H., additional, and Bogan, M.J., additional

Published
2012
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21. Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography

Author

Redecke, L., primary, Nass, K., additional, DePonte, D.P., additional, White, T.A., additional, Rehders, D., additional, Barty, A., additional, Stellato, F., additional, Liang, M., additional, Barends, T.R.M., additional, Boutet, S., additional, Williams, G.W., additional, Messerschmidt, M., additional, Seibert, M.M., additional, Aquila, A., additional, Arnlund, D., additional, Bajt, S., additional, Barth, T., additional, Bogan, M.J., additional, Caleman, C., additional, Chao, T.-C., additional, Doak, R.B., additional, Fleckenstein, H., additional, Frank, M., additional, Fromme, R., additional, Galli, L., additional, Grotjohann, I., additional, Hunter, M.S., additional, Johansson, L.C., additional, Kassemeyer, S., additional, Katona, G., additional, Kirian, R.A., additional, Koopmann, R., additional, Kupitz, C., additional, Lomb, L., additional, Martin, A.V., additional, Mogk, S., additional, Neutze, R., additional, Shoemann, R.L., additional, Steinbrener, J., additional, Timneanu, N., additional, Wang, D., additional, Weierstall, U., additional, Zatsepin, N.A., additional, Spence, J.C.H., additional, Fromme, P., additional, Schlichting, I., additional, Duszenko, M., additional, Betzel, C., additional, and Chapman, H., additional

Published
2012
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22. Erratum: Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

Author

Loh, N. D., primary, Hampton, C. Y., additional, Martin, A. V., additional, Starodub, D., additional, Sierra, R. G., additional, Barty, A., additional, Aquila, A., additional, Schulz, J., additional, Lomb, L., additional, Steinbrener, J., additional, Shoeman, R. L., additional, Kassemeyer, S., additional, Bostedt, C., additional, Bozek, J., additional, Epp, S. W., additional, Erk, B., additional, Hartmann, R., additional, Rolles, D., additional, Rudenko, A., additional, Rudek, B., additional, Foucar, L., additional, Kimmel, N., additional, Weidenspointner, G., additional, Hauser, G., additional, Holl, P., additional, Pedersoli, E., additional, Liang, M., additional, Hunter, M. S., additional, Gumprecht, L., additional, Coppola, N., additional, Wunderer, C., additional, Graafsma, H., additional, Maia, F. R. N. C., additional, Ekeberg, T., additional, Hantke, M., additional, Fleckenstein, H., additional, Hirsemann, H., additional, Nass, K., additional, White, T. A., additional, Tobias, H. J., additional, Farquar, G. R., additional, Benner, W. H., additional, Hau-Riege, S. P., additional, Reich, C., additional, Hartmann, A., additional, Soltau, H., additional, Marchesini, S., additional, Bajt, S., additional, Barthelmess, M., additional, Bucksbaum, P., additional, Hodgson, K. O., additional, Strüder, L., additional, Ullrich, J., additional, Frank, M., additional, Schlichting, I., additional, Chapman, H. N., additional, and Bogan, M. J., additional

Published
2012
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23. Noise-robust coherent diffractive imaging with a single diffraction pattern

Author

Martin, A. V., primary, Wang, F., additional, Loh, N. D., additional, Ekeberg, T., additional, Maia, F. R. N. C., additional, Hantke, M., additional, van der Schot, G., additional, Hampton, C. Y., additional, Sierra, R. G., additional, Aquila, A., additional, Bajt, S., additional, Barthelmess, M., additional, Bostedt, C., additional, Bozek, J. D., additional, Coppola, N., additional, Epp, S. W., additional, Erk, B., additional, Fleckenstein, H., additional, Foucar, L., additional, Frank, M., additional, Graafsma, H., additional, Gumprecht, L., additional, Hartmann, A., additional, Hartmann, R., additional, Hauser, G., additional, Hirsemann, H., additional, Holl, P., additional, Kassemeyer, S., additional, Kimmel, N., additional, Liang, M., additional, Lomb, L., additional, Marchesini, S., additional, Nass, K., additional, Pedersoli, E., additional, Reich, C., additional, Rolles, D., additional, Rudek, B., additional, Rudenko, A., additional, Schulz, J., additional, Shoeman, R. L., additional, Soltau, H., additional, Starodub, D., additional, Steinbrener, J., additional, Stellato, F., additional, Strüder, L., additional, Ullrich, J., additional, Weidenspointner, G., additional, White, T. A., additional, Wunderer, C. B., additional, Barty, A., additional, Schlichting, I., additional, Bogan, M. J., additional, and Chapman, H. N., additional

Published
2012
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24. Lysozyme, room temperature, 400 kGy dose

Author

Boutet, S., primary, Lomb, L., additional, Williams, G., additional, Barends, T., additional, Aquila, A., additional, Doak, R.B., additional, Weierstall, U., additional, DePonte, D., additional, Steinbrener, J., additional, Shoeman, R., additional, Messerschmidt, M., additional, Barty, A., additional, White, T., additional, Kassemeyer, S., additional, Kirian, R., additional, Seibert, M., additional, Montanez, P., additional, Kenney, C., additional, Herbst, R., additional, Hart, P., additional, Pines, J., additional, Haller, G., additional, Gruner, S., additional, Philllip, H., additional, Tate, M., additional, Hromalik, M., additional, Koerner, L., additional, van Bakel, N., additional, Morse, J., additional, Ghonsalves, W., additional, Arnlund, D., additional, Bogan, M., additional, Calemann, C., additional, Fromme, R., additional, Hampton, C., additional, Hunter, M., additional, Johansson, L., additional, Katona, G., additional, Kupitz, C., additional, Liang, M., additional, Martin, A., additional, Nass, K., additional, Redecke, L., additional, Stellato, F., additional, Timneanu, N., additional, Wang, D., additional, Zatsepin, N., additional, Schafer, D., additional, Defever, K., additional, Neutze, R., additional, Fromme, P., additional, Spence, J., additional, Chapman, H., additional, and Schlichting, I., additional

Published
2012
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25. Lysozyme, room temperature, 24 kGy dose

Author

Boutet, S., primary, Lomb, L., additional, Williams, G., additional, Barends, T., additional, Aquila, A., additional, Doak, R.B., additional, Weierstall, U., additional, DePonte, D., additional, Steinbrener, J., additional, Shoeman, R., additional, Messerschmidt, M., additional, Barty, A., additional, White, T., additional, Kassemeyer, S., additional, Kirian, R., additional, Seibert, M., additional, Montanez, P., additional, Kenney, C., additional, Herbst, R., additional, Hart, P., additional, Pines, J., additional, Haller, G., additional, Gruner, S., additional, Philllip, H., additional, Tate, M., additional, Hromalik, M., additional, Koerner, L., additional, van Bakel, N., additional, Morse, J., additional, Ghonsalves, W., additional, Arnlund, D., additional, Bogan, M., additional, Calemann, C., additional, Fromme, R., additional, Hampton, C., additional, Hunter, M., additional, Johansson, L., additional, Katona, G., additional, Kupitz, C., additional, Liang, M., additional, Martin, A., additional, Nass, K., additional, Redecke, L., additional, Stellato, F., additional, Timneanu, N., additional, Wang, D., additional, Zatsepin, N., additional, Schafer, D., additional, Defever, K., additional, Neutze, R., additional, Fromme, P., additional, Spence, J., additional, Chapman, H., additional, and Schlichting, I., additional

Published
2012
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26. Lysozyme, room-temperature, rotating anode, 0.0021 MGy

Author

Boutet, S., primary, Lomb, L., additional, Williams, G., additional, Barends, T., additional, Aquila, A., additional, Doak, R.B., additional, Weierstall, U., additional, DePonte, D., additional, Steinbrener, J., additional, Shoeman, R., additional, Messerschmidt, M., additional, Barty, A., additional, White, T., additional, Kassemeyer, S., additional, Kirian, R., additional, Seibert, M., additional, Montanez, P., additional, Kenney, C., additional, Herbst, R., additional, Hart, P., additional, Pines, J., additional, Haller, G., additional, Gruner, S., additional, Philllip, H., additional, Tate, M., additional, Hromalik, M., additional, Koerner, L., additional, van Bakel, N., additional, Morse, J., additional, Ghonsalves, W., additional, Arnlund, D., additional, Bogan, M., additional, Calemann, C., additional, Fromme, R., additional, Hampton, C., additional, Hunter, M., additional, Johansson, L., additional, Katona, G., additional, Kupitz, C., additional, Liang, M., additional, Martin, A., additional, Nass, K., additional, Redecke, L., additional, Stellato, F., additional, Timneanu, N., additional, Wang, D., additional, Zatsepin, N., additional, Schafer, D., additional, Defever, K., additional, Neutze, R., additional, Fromme, P., additional, Spence, J., additional, Chapman, H., additional, and Schlichting, I., additional

Published
2012
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27. Hen egg-white lysozyme solved from 40 fs free-electron laser pulse data

Author

Boutet, S., primary, Lomb, L., additional, Williams, G., additional, Barends, T., additional, Aquila, A., additional, Doak, R.B., additional, Weierstall, U., additional, DePonte, D., additional, Steinbrener, J., additional, Shoeman, R., additional, Messerschmidt, M., additional, Barty, A., additional, White, T., additional, Kassemeyer, S., additional, Kirian, R., additional, Seibert, M., additional, Montanez, P., additional, Kenney, C., additional, Herbst, R., additional, Hart, P., additional, Pines, J., additional, Haller, G., additional, Gruner, S., additional, Philllip, H., additional, Tate, M., additional, Hromalik, M., additional, Koerner, L., additional, van Bakel, N., additional, Morse, J., additional, Ghonsalves, W., additional, Arnlund, D., additional, Bogan, M., additional, Calemann, C., additional, Fromme, R., additional, Hampton, C., additional, Hunter, M., additional, Johansson, L., additional, Katona, G., additional, Kupitz, C., additional, Liang, M., additional, Martin, A., additional, Nass, K., additional, Redecke, L., additional, Stellato, F., additional, Timneanu, N., additional, Wang, D., additional, Zatsepin, N., additional, Schafer, D., additional, Defever, K., additional, Neutze, R., additional, Fromme, P., additional, Spence, J., additional, Chapman, H., additional, and Schlichting, I., additional

Published
2012
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28. Hen egg-white lysozyme solved from 5 fs free-electron laser pulse data

Author

Boutet, S., primary, Lomb, L., additional, Williams, G., additional, Barends, T., additional, Aquila, A., additional, Doak, R.B., additional, Weierstall, U., additional, DePonte, D., additional, Steinbrener, J., additional, Shoeman, R., additional, Messerschmidt, M., additional, Barty, A., additional, White, T., additional, Kassemeyer, S., additional, Kirian, R., additional, Seibert, M., additional, Montanez, P., additional, Kenney, C., additional, Herbst, R., additional, Hart, P., additional, Pines, J., additional, Haller, G., additional, Gruner, S., additional, Philllip, H., additional, Tate, M., additional, Hromalik, M., additional, Koerner, L., additional, van Bakel, N., additional, Morse, J., additional, Ghonsalves, W., additional, Arnlund, D., additional, Bogan, M., additional, Calemann, C., additional, Fromme, R., additional, Hampton, C., additional, Hunter, M., additional, Johansson, L., additional, Katona, G., additional, Kupitz, C., additional, Liang, M., additional, Martin, A., additional, Nass, K., additional, Redecke, L., additional, Stellato, F., additional, Timneanu, N., additional, Wang, D., additional, Zatsepin, N., additional, Schafer, D., additional, Defever, K., additional, Neutze, R., additional, Fromme, P., additional, Spence, J., additional, Chapman, H., additional, and Schlichting, I., additional

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2012
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29. Femtosecond dark-field imaging with an X-ray free electron laser

Author

Martin, A.V., primary, Loh, N.D., additional, Hampton, C.Y., additional, Sierra, R.G., additional, Wang, F., additional, Aquila, A., additional, Bajt, S., additional, Barthelmess, M., additional, Bostedt, C., additional, Bozek, J.D., additional, Coppola, N., additional, Epp, S.W., additional, Erk, B., additional, Fleckenstein, H., additional, Foucar, L., additional, Frank, M., additional, Graafsma, H., additional, Gumprecht, L., additional, Hartmann, A., additional, Hartmann, R., additional, Hauser, G., additional, Hirsemann, H., additional, Holl, P., additional, Kassemeyer, S., additional, Kimmel, N., additional, Liang, M., additional, Lomb, L., additional, Maia, F.R.N.C., additional, Marchesini, S., additional, Nass, K., additional, Pedersoli, E., additional, Reich, C., additional, Rolles, D., additional, Rudek, B., additional, Rudenko, A., additional, Schulz, J., additional, Shoeman, R.L., additional, Soltau, H., additional, Starodub, D., additional, Steinbrener, J., additional, Stellato, F., additional, Strüder, L., additional, Ullrich, J., additional, Weidenspointner, G., additional, White, T.A., additional, Wunderer, C.B., additional, Barty, A., additional, Schlichting, I., additional, Bogan, M.J., additional, and Chapman, H.N., additional

Published
2012
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30. Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography

Author

Johansson, L.C., primary, Arnlund, D., additional, White, T.A., additional, Katona, G., additional, DePonte, D.P., additional, Weierstall, U., additional, Doak, R.B., additional, Shoeman, R.L., additional, Lomb, L., additional, Malmerberg, E., additional, Davidsson, J., additional, Nass, K., additional, Liang, M., additional, Andreasson, J., additional, Aquila, A., additional, Bajt, S., additional, Barthelmess, M., additional, Barty, A., additional, Bogan, M.J., additional, Bostedt, C., additional, Bozek, J.D., additional, Caleman, C., additional, Coffee, R., additional, Coppola, N., additional, Ekeberg, T., additional, Epp, S.W., additional, Erk, B., additional, Fleckenstein, H., additional, Foucar, L., additional, Graafsma, H., additional, Gumprecht, L., additional, Hajdu, J., additional, Hampton, C.Y., additional, Hartmann, R., additional, Hartmann, A., additional, Hauser, G., additional, Hirsemann, H., additional, Holl, P., additional, Hunter, M.S., additional, Kassemeyer, S., additional, Kimmel, N., additional, Kirian, R.A., additional, Maia, F.R.N.C., additional, Marchesini, S., additional, Martin, A.V., additional, Reich, C., additional, Rolles, D., additional, Rudek, B., additional, Rudenko, A., additional, Schlichting, I., additional, Schulz, J., additional, Seibert, M.M., additional, Sierra, R., additional, Soltau, H., additional, Starodub, D., additional, Stellato, F., additional, Stern, S., additional, Struder, L., additional, Timneanu, N., additional, Ullrich, J., additional, Wahlgren, W.Y., additional, Wang, X., additional, Weidenspointner, G., additional, Wunderer, C., additional, Fromme, P., additional, Chapman, H.N., additional, Spence, J.C.H., additional, and Neutze, R., additional

Published
2012
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31. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Author

Nass, Karol, Redecke, Lars, Perbandt, Markus, Yefanov, O., Klinge, M., Koopmann, R., Stellato, F., Gabdulkhakov, A., Schönherr, R., Rehders, D., Lahey-Rudolph, J. M., Aquila, A., Barty, A., Basu, Shibom, Doak, R. Bruce, Duden, R., Frank, Matthias, Fromme, Raimund, Kassemeyer, S., Katona, Gergely, Kirian, Richard, Liu, H., Majoul, I., Martin-Garcia, J. M., Messerschmidt, M., Shoeman, R. L., Weierstall, U., Westenhoff, S., White, Thomas, Williams, G. J., Yoon, C. H., Zatsepin, Nadia, Fromme, P., Duszenko, M., Chapman, H. N., and Betzel, C.

Subjects
3. Good health
Abstract

Nature Communications 11(1), 620 (2020). doi:10.1038/s41467-020-14484-w, Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds., Published by Nature Publishing Group UK, [London]

33. Free-electron laser data for multiple-particle fluctuation scattering analysis.

Author

Pande K, Donatelli JJ, Malmerberg E, Foucar L, Poon BK, Sutter M, Botha S, Basu S, Bruce Doak R, Dörner K, Epp SW, Englert L, Fromme R, Hartmann E, Hartmann R, Hauser G, Hattne J, Hosseinizadeh A, Kassemeyer S, Lomb L, Montero SFC, Menzel A, Rolles D, Rudenko A, Seibert MM, Sierra RG, Schwander P, Ourmazd A, Fromme P, Sauter NK, Bogan M, Bozek J, Bostedt C, Schlichting I, Kerfeld CA, and Zwart PH

Subjects
Phycodnaviridae, Scattering, Small Angle, X-Ray Diffraction
Abstract

Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which solution scattering data are collected using X-ray exposures below rotational diffusion times, resulting in angularly anisotropic X-ray snapshots that provide several orders of magnitude more information than traditional solution scattering data. Such experiments can be performed using the ultrashort X-ray pulses provided by a free-electron laser source, allowing one to collect a large number of diffraction patterns in a relatively short time. Here, we describe a test data set for FXS, obtained at the Linac Coherent Light Source, consisting of close to 100 000 multi-particle diffraction patterns originating from approximately 50 to 200 Paramecium Bursaria Chlorella virus particles per snapshot. In addition to the raw data, a selection of high-quality pre-processed diffraction patterns and a reference SAXS profile are provided.

Published
2018
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34. Corrigendum: Diffraction data of core-shell nanoparticles from an X-ray free electron laser.

Author

Li X, Chiu CY, Wang HJ, Kassemeyer S, Botha S, Shoeman RL, Lawrence RM, Kupitz C, Kirian R, James D, Wang D, Nelson G, Messerschmidt M, Boutet S, Williams GJ, Hartmann E, Jafarpour A, Foucar LM, Barty A, Chapman H, Liang M, Menzel A, Wang F, Basu S, Fromme R, Doak RB, Fromme P, Weierstall U, Huang MH, Spence JCH, Schlichting I, Hogue BG, and Liu H

Abstract

This corrects the article DOI: 10.1038/sdata.2017.48.

Published
2017
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35. Diffraction data of core-shell nanoparticles from an X-ray free electron laser.

Author

Li X, Chiu CY, Wang HJ, Kassemeyer S, Botha S, Shoeman RL, Lawrence RM, Kupitz C, Kirian R, James D, Wang D, Nelson G, Messerschmidt M, Boutet S, Williams GJ, Hartmann E, Jafarpour A, Foucar LM, Barty A, Chapman H, Liang M, Menzel A, Wang F, Basu S, Fromme R, Doak RB, Fromme P, Weierstall U, Huang MH, Spence JC, Schlichting I, Hogue BG, and Liu H

Abstract

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.

Published
2017
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36. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser.

Author

Ekeberg T, Svenda M, Seibert MM, Abergel C, Maia FR, Seltzer V, DePonte DP, Aquila A, Andreasson J, Iwan B, Jönsson O, Westphal D, Odić D, Andersson I, Barty A, Liang M, Martin AV, Gumprecht L, Fleckenstein H, Bajt S, Barthelmess M, Coppola N, Claverie JM, Loh ND, Bostedt C, Bozek JD, Krzywinski J, Messerschmidt M, Bogan MJ, Hampton CY, Sierra RG, Frank M, Shoeman RL, Lomb L, Foucar L, Epp SW, Rolles D, Rudenko A, Hartmann R, Hartmann A, Kimmel N, Holl P, Weidenspointner G, Rudek B, Erk B, Kassemeyer S, Schlichting I, Strüder L, Ullrich J, Schmidt C, Krasniqi F, Hauser G, Reich C, Soltau H, Schorb S, Hirsemann H, Wunderer C, Graafsma H, Chapman H, and Hajdu J

Subjects
Algorithms, Computer Simulation, Crystallography, X-Ray, Data Collection, Electrons, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Lasers, Models, Theoretical, Particle Size, Scattering, Radiation, X-Rays, Mimiviridae, X-Ray Diffraction
Abstract

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

Published
2016
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37. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams.

Author

Nass K, Foucar L, Barends TR, Hartmann E, Botha S, Shoeman RL, Doak RB, Alonso-Mori R, Aquila A, Bajt S, Barty A, Bean R, Beyerlein KR, Bublitz M, Drachmann N, Gregersen J, Jönsson HO, Kabsch W, Kassemeyer S, Koglin JE, Krumrey M, Mattle D, Messerschmidt M, Nissen P, Reinhard L, Sitsel O, Sokaras D, Williams GJ, Hau-Riege S, Timneanu N, Caleman C, Chapman HN, Boutet S, and Schlichting I

Subjects
Clostridium radiation effects, Crystallography, X-Ray methods, Dose-Response Relationship, Radiation, Humans, Models, Molecular, Radiation Injuries, Sensitivity and Specificity, Ferredoxins radiation effects, Metalloproteins radiation effects, Synchrotrons
Abstract

Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

Published
2015
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38. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

Author

Kupitz C, Basu S, Grotjohann I, Fromme R, Zatsepin NA, Rendek KN, Hunter MS, Shoeman RL, White TA, Wang D, James D, Yang JH, Cobb DE, Reeder B, Sierra RG, Liu H, Barty A, Aquila AL, Deponte D, Kirian RA, Bari S, Bergkamp JJ, Beyerlein KR, Bogan MJ, Caleman C, Chao TC, Conrad CE, Davis KM, Fleckenstein H, Galli L, Hau-Riege SP, Kassemeyer S, Laksmono H, Liang M, Lomb L, Marchesini S, Martin AV, Messerschmidt M, Milathianaki D, Nass K, Ros A, Roy-Chowdhury S, Schmidt K, Seibert M, Steinbrener J, Stellato F, Yan L, Yoon C, Moore TA, Moore AL, Pushkar Y, Williams GJ, Boutet S, Doak RB, Weierstall U, Frank M, Chapman HN, Spence JC, and Fromme P

Subjects
Protein Structure, Tertiary, Crystallography, X-Ray, Cyanobacteria chemistry, Models, Molecular, Photosystem II Protein Complex chemistry
Abstract

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

Published
2014
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39. Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers.

Author

Park HJ, Loh ND, Sierra RG, Hampton CY, Starodub D, Martin AV, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Lomb L, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FR, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ, and Elser V

Abstract

Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

Published
2013
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40. Optimal mapping of x-ray laser diffraction patterns into three dimensions using routing algorithms.

Author

Kassemeyer S, Jafarpour A, Lomb L, Steinbrener J, Martin AV, and Schlichting I

Subjects
Photons, Rotation, Algorithms, Image Processing, Computer-Assisted methods, Lasers, X-Ray Diffraction
Abstract

Coherent diffractive imaging with x-ray free-electron lasers (XFEL) promises high-resolution structure determination of noncrystalline objects. Randomly oriented particles are exposed to XFEL pulses for acquisition of two-dimensional (2D) diffraction snapshots. The knowledge of their orientations enables 3D imaging by multiview reconstruction, combining 2D diffraction snapshots in different orientations. Here we introduce a globally optimal algorithm that can infer these orientations. We apply it to experimental XFEL data of nanoparticles and so determine their 3D electron density.

Published
2013
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41. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres.

Author

Loh ND, Starodub D, Lomb L, Hampton CY, Martin AV, Sierra RG, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FR, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, and Bogan MJ

Subjects
Electrons, Equipment Design, Equipment Failure Analysis, Microspheres, Aerosols analysis, Aerosols chemistry, Lasers, Photometry methods, Refractometry methods, Surface Plasmon Resonance methods, X-Rays
Abstract

Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.

Published
2013
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42. Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser.

Author

Barends TR, Foucar L, Shoeman RL, Bari S, Epp SW, Hartmann R, Hauser G, Huth M, Kieser C, Lomb L, Motomura K, Nagaya K, Schmidt C, Strecker R, Anielski D, Boll R, Erk B, Fukuzawa H, Hartmann E, Hatsui T, Holl P, Inubushi Y, Ishikawa T, Kassemeyer S, Kaiser C, Koeck F, Kunishima N, Kurka M, Rolles D, Rudek B, Rudenko A, Sato T, Schroeter CD, Soltau H, Strueder L, Tanaka T, Togashi T, Tono K, Ullrich J, Yase S, Wada SI, Yao M, Yabashi M, Ueda K, and Schlichting I

Subjects
Crystallography, X-Ray instrumentation, Cysteine chemistry, Models, Molecular, Muramidase chemistry, Crystallography, X-Ray methods, Lasers, Protein Conformation, Sulfur chemistry
Abstract

X-ray free-electron lasers (FELs) enable crystallographic data collection using extremely bright femtosecond pulses from microscopic crystals beyond the limitations of conventional radiation damage. This diffraction-before-destruction approach requires a new crystal for each FEL shot and, since the crystals cannot be rotated during the X-ray pulse, data collection requires averaging over many different crystals and a Monte Carlo integration of the diffraction intensities, making the accurate determination of structure factors challenging. To investigate whether sufficient accuracy can be attained for the measurement of anomalous signal, a large data set was collected from lysozyme microcrystals at the newly established `multi-purpose spectroscopy/imaging instrument' of the SPring-8 Ångstrom Compact Free-Electron Laser (SACLA) at RIKEN Harima. Anomalous difference density maps calculated from these data demonstrate that serial femtosecond crystallography using a free-electron laser is sufficiently accurate to measure even the very weak anomalous signal of naturally occurring S atoms in a protein at a photon energy of 7.3 keV.

Published
2013
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43. Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.

Author

Redecke L, Nass K, DePonte DP, White TA, Rehders D, Barty A, Stellato F, Liang M, Barends TRM, Boutet S, Williams GJ, Messerschmidt M, Seibert MM, Aquila A, Arnlund D, Bajt S, Barth T, Bogan MJ, Caleman C, Chao TC, Doak RB, Fleckenstein H, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Johansson LC, Kassemeyer S, Katona G, Kirian RA, Koopmann R, Kupitz C, Lomb L, Martin AV, Mogk S, Neutze R, Shoeman RL, Steinbrener J, Timneanu N, Wang D, Weierstall U, Zatsepin NA, Spence JCH, Fromme P, Schlichting I, Duszenko M, Betzel C, and Chapman HN

Subjects
Amino Acid Sequence, Animals, Catalytic Domain, Cathepsin B antagonists & inhibitors, Crystallization, Crystallography, X-Ray, Enzyme Precursors chemistry, Glycosylation, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protozoan Proteins antagonists & inhibitors, Sf9 Cells, Spodoptera, X-Rays, Cathepsin B chemistry, Protozoan Proteins chemistry, Trypanosoma brucei brucei enzymology
Abstract

The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.

Published
2013
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44. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.

Author

Johansson LC, Arnlund D, Katona G, White TA, Barty A, DePonte DP, Shoeman RL, Wickstrand C, Sharma A, Williams GJ, Aquila A, Bogan MJ, Caleman C, Davidsson J, Doak RB, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Kassemeyer S, Kirian RA, Kupitz C, Liang M, Lomb L, Malmerberg E, Martin AV, Messerschmidt M, Nass K, Redecke L, Seibert MM, Sjöhamn J, Steinbrener J, Stellato F, Wang D, Wahlgren WY, Weierstall U, Westenhoff S, Zatsepin NA, Boutet S, Spence JC, Schlichting I, Chapman HN, Fromme P, and Neutze R

Subjects
Protein Conformation, Crystallography, X-Ray methods, Hyphomicrobiaceae chemistry, Photosynthetic Reaction Center Complex Proteins chemistry
Abstract

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

Published
2013
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45. Femtosecond free-electron laser x-ray diffraction data sets for algorithm development.

Author

Kassemeyer S, Steinbrener J, Lomb L, Hartmann E, Aquila A, Barty A, Martin AV, Hampton CY, Bajt S, Barthelmess M, Barends TR, Bostedt C, Bott M, Bozek JD, Coppola N, Cryle M, DePonte DP, Doak RB, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Hömke A, Holl P, Jönsson O, Kimmel N, Krasniqi F, Liang M, Maia FR, Marchesini S, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schmidt C, Schulz J, Shoeman RL, Sierra RG, Soltau H, Spence JC, Starodub D, Stellato F, Stern S, Stier G, Svenda M, Weidenspointner G, Weierstall U, White TA, Wunderer C, Frank M, Chapman HN, Ullrich J, Strüder L, Bogan MJ, and Schlichting I

Abstract

We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.

Published
2012
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46. Time-resolved protein nanocrystallography using an X-ray free-electron laser.

Author

Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt S, Barends TR, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, Caleman C, Coppola N, Davidsson J, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel KU, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FR, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JC, and Chapman HN

Subjects
Electrons, Protein Conformation, X-Rays, Crystallography, X-Ray methods, Ferredoxins ultrastructure, Lasers, Nanostructures ultrastructure, X-Ray Diffraction methods
Abstract

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

Published
2012
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47. In vivo protein crystallization opens new routes in structural biology.

Author

Koopmann R, Cupelli K, Redecke L, Nass K, Deponte DP, White TA, Stellato F, Rehders D, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Boutet S, Bozek JD, Caleman C, Coppola N, Davidsson J, Doak RB, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kirian RA, Lomb L, Maia FR, Kimmel N, Martin AV, Messerschmidt M, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Williams GJ, Wunderer CB, Fromme P, Spence JC, Stehle T, Chapman HN, Betzel C, and Duszenko M

Subjects
Protein Binding radiation effects, Protein Conformation radiation effects, Proteins radiation effects, Solubility radiation effects, X-Rays, Crystallography methods, Crystallography, X-Ray methods, Proteins chemistry, Proteins ultrastructure
Abstract

Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

Published
2012
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48. Lipidic phase membrane protein serial femtosecond crystallography.

Author

Johansson LC, Arnlund D, White TA, Katona G, Deponte DP, Weierstall U, Doak RB, Shoeman RL, Lomb L, Malmerberg E, Davidsson J, Nass K, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kimmel N, Kirian RA, Maia FR, Marchesini S, Martin AV, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Sierra RG, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wahlgren WY, Wang X, Weidenspointner G, Wunderer C, Fromme P, Chapman HN, Spence JC, and Neutze R

Subjects
Protein Binding, Protein Conformation radiation effects, X-Rays, Crystallography, X-Ray methods, Lipid Bilayers chemistry, Membrane Proteins chemistry, Membrane Proteins ultrastructure
Abstract

X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

Published
2012
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49. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering.

Author

Yoon CH, Schwander P, Abergel C, Andersson I, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek J, Chapman HN, Claverie JM, Coppola N, DePonte DP, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann E, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Kiskinova M, Liang M, Loh NT, Lomb L, Maia FR, Martin AV, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert M, Seltzer V, Shoeman RL, Sierra RG, Soltau H, Starodub D, Steinbrener J, Stier G, Strüder L, Svenda M, Ullrich J, Weidenspointner G, White TA, Wunderer C, and Ourmazd A

Abstract

Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification., (© 2011 Optical Society of America)

Published
2011
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