The recent development of X-ray free-electron laser sources has created new 
opportunities for the structural analysis of protein nanocrystals. The extremely 
small sizes of the crystals, as well as imperfections of the crystal structure, 
result in an interference phenomenon in the diffraction pattern. With decreasing 
crystallite size the structural imperfections play a role in the formation of 
the diffraction pattern that is comparable in importance to the size effects and 
should be taken into account during the data analysis and structure 
reconstruction processes. There now exists a need to develop new methods of 
protein structure determination that do not depend on the availability of 
good-quality crystals and that can treat proteins under conditions close to the 
active form. This paper demonstrates an approach that is specifically tailored 
to nanocrystalline samples and offers a unique crystallographic solution.