Statistically correcting dynamical electron scattering improves refinement of protein nanocrystals, including charge refinement of coordinated metals
Thorsten B. Blum, Dominique Housset, Max T.B. Clabbers, Eric van Genderen, Maria Bacia-Verloop, Ulrich Zander, Andrew A. McCarthy, Guy Schoehn, Wai Li Ling, Jan Pieter Abrahams [1]
Molecular Tour
Electron crystallography employs standard transmission electron microscopes as opposed to large-scale facilities for X-ray or neutron. It is also more sensitive to atomic charges, which are important for understanding enzyme catalysis and other protein functions. Besides, only nanosized crystals are required. Nevertheless, the strong interaction with matter means that electron multiple scattering is non-negligible, which complicates structure determination.
Taking into consideration the effect of multiple scattering, we correct the diffraction intensities using a likelihood-based algorithm. As shown in the figures (Figure 2 and Figure 4 in the manuscript), this method has improved the resulting structure and has permitted us to estimate the charge of the Zn ion in the thermolysin and insulin crystals.
The atomic model of insulin at one of the Zn ion sites for different assigned Zn charge states:
The atomic model of thermolysin showing the active site with the Zn ion:
The atomic model of Thaumatin with Cl ion:
PDB references: insulin, electron diffraction data, 6zhb; X-ray diffraction data, 6zi8; thermolysin, electron diffraction data, 6zhj; thaumatin, electron diffraction data, 6zhn.
References
- ↑ Blum TB, Housset D, Clabbers MTB, van Genderen E, Bacia-Verloop M, Zander U, McCarthy AA, Schoehn G, Ling WL, Abrahams JP. Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals. Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):75-85. doi:, 10.1107/S2059798320014540. Epub 2021 Jan 1. PMID:33404527 doi:http://dx.doi.org/10.1107/S2059798320014540
