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Low-energy nuclear reactions are known to be extremely dependent on the local crystal structure and crystal defects of the deuterated samples. This has a strong influence on both hydrogen diffusion and the effective electron mass. The latter determines the strength of the local electron-screening effect and can change the deuteron–deuteron reaction rates at very low energies by many orders of magnitude. In the present study, zirconium samples were exposed to various conditions and energies of deuteron beams using the unique accelerator system with ultra-high vacuum, installed in the eLBRUS laboratory at the University of Szczecin. Irradiated and virgin samples were investigated by means of the X-ray diffraction (XRD) and positron annihilation spectroscopy (PAS). While the first method delivers information about changes of crystal lattice parameters and possible production of hydrides accompanying the formation of dislocations that are produced during irradiation of the samples, the second one can determine the depth distribution of crystal defects, being especially sensitive to vacancies. The studied Zr samples were also implanted by carbon and oxygen ions in order to simulate the real situation taking place in nuclear reaction experiments and to investigate their influence on the kinetic of produced vacancies. The observed enhancement of the electron-screening effect in the deuteron fusion reaction at very low energies could be explained by formation of a high number of vacancies during the deuteron irradiation of samples. Possible carbon and oxygen impurities can affect this process in various ways by changing the depth distribution of vacancies and their diffusion, but they play only a minor role in the strength of the electron-screening effect. [ABSTRACT FROM AUTHOR]