Statistically correcting dynamical electron scattering improves refinement of protein nanocrystals, including charge refinement of coordinated metals

Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, we limited dynamical scattering of nanocrystals of insulin, thermolysin, and thaumatin by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, we used a low-noise hybrid-pixel Timepix electron counting detector. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which we introduced previously for analyzing electron diffraction data of small molecule nanocrystals and adapted here for protein crystals. We show that the procedure notably improved the structural refinement, allowing in one case the location of solvent molecules. It also allowed the refinement of the charge state of bound metal atoms, an important element in protein functions, through B-factor analysis of the metal atoms and their ligands. Our results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.