[en] X-ray holography scheme with reference scatterer consisting of heavy atom as reference center and its link to an object consisting of several light atoms and using controlled variation of the alignment is represented. The scheme can reproduce an object in three dimensions with atomic resolution. The distorting factors of reconstruction are considered. - Highlights: • X-ray holography scheme with a reference wave formed by atomic scatterer. • 3D object reconstruction with atomic resolution from the set of holograms. • Simple formula for the distorting factor in reconstruction.