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Statistically correcting dynamical electron scattering improves the 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, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave a...

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Autores principales: Blum, Thorsten B., Housset, Dominique, Clabbers, Max T. B., van Genderen, Eric, Bacia-Verloop, Maria, Zander, Ulrich, McCarthy, Andrew A., Schoehn, Guy, Ling, Wai Li, Abrahams, Jan Pieter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787111/
https://www.ncbi.nlm.nih.gov/pubmed/33404527
http://dx.doi.org/10.1107/S2059798320014540
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author Blum, Thorsten B.
Housset, Dominique
Clabbers, Max T. B.
van Genderen, Eric
Bacia-Verloop, Maria
Zander, Ulrich
McCarthy, Andrew A.
Schoehn, Guy
Ling, Wai Li
Abrahams, Jan Pieter
author_facet Blum, Thorsten B.
Housset, Dominique
Clabbers, Max T. B.
van Genderen, Eric
Bacia-Verloop, Maria
Zander, Ulrich
McCarthy, Andrew A.
Schoehn, Guy
Ling, Wai Li
Abrahams, Jan Pieter
author_sort Blum, Thorsten B.
collection PubMed
description 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.
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spelling pubmed-77871112021-01-29 Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals Blum, Thorsten B. Housset, Dominique Clabbers, Max T. B. van Genderen, Eric Bacia-Verloop, Maria Zander, Ulrich McCarthy, Andrew A. Schoehn, Guy Ling, Wai Li Abrahams, Jan Pieter Acta Crystallogr D Struct Biol Research Papers 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. International Union of Crystallography 2021-01-01 /pmc/articles/PMC7787111/ /pubmed/33404527 http://dx.doi.org/10.1107/S2059798320014540 Text en © Blum et al. 2021 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Research Papers
Blum, Thorsten B.
Housset, Dominique
Clabbers, Max T. B.
van Genderen, Eric
Bacia-Verloop, Maria
Zander, Ulrich
McCarthy, Andrew A.
Schoehn, Guy
Ling, Wai Li
Abrahams, Jan Pieter
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
title Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
title_full Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
title_fullStr Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
title_full_unstemmed Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
title_short Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
title_sort statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787111/
https://www.ncbi.nlm.nih.gov/pubmed/33404527
http://dx.doi.org/10.1107/S2059798320014540
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