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

被引:16
作者
Blum, Thorsten B. [1 ]
Housset, Dominique [2 ]
Clabbers, Max T. B. [3 ,5 ]
van Genderen, Eric [1 ]
Bacia-Verloop, Maria [2 ]
Zander, Ulrich [4 ]
McCarthy, Andrew A. [4 ]
Schoehn, Guy [2 ]
Ling, Wai Li [2 ]
Abrahams, Jan Pieter [1 ,3 ]
机构
[1] Paul Scherrer Inst, Dept Biol & Chem, CH-5232 Villigen, Switzerland
[2] Univ Grenoble Alpes, IBS, CNRS, CEA, 71 Ave Martyrs, F-38000 Grenoble, France
[3] Univ Basel, Ctr Cellular Imaging & NanoAnalyt C CINA, Biozentrum, Mattenstr 26, CH-4058 Basel, Switzerland
[4] European Mol Biol Lab, 71 Ave Martyrs, F-38042 Grenoble, France
[5] Stockholm Univ, Dept Mat & Environm Chem, S-10691 Stockholm, Sweden
来源
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2021年 / 77卷
基金
瑞士国家科学基金会;
关键词
electron diffraction; dynamical scattering; protein; nanocrystals; likelihood-based correction; DIFFRACTION; CRYSTALLOGRAPHY; CRYSTALS; MICROSCOPY;
D O I
10.1107/S2059798320014540
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is 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, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, a low-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.
引用
收藏
页码:75 / 85
页数:11
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