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Real-space quantum-based refinement for cryo-EM: Q|R#3

Lum Wang, Holger Kruse, Oleg V. Sobolev, View ORCID ProfileNigel W. Moriarty, Mark P. Waller, View ORCID ProfilePavel V. Afonine, Malgorzata Biczysko
doi: https://doi.org/10.1101/2020.05.25.115386
Lum Wang
1International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
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Holger Kruse
2Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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Oleg V. Sobolev
3Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Nigel W. Moriarty
3Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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  • ORCID record for Nigel W. Moriarty
Mark P. Waller
4Pending AI Pty Ltd., iAccelerate, Innovation Campus, North Wollongong, 2500, Australia
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Pavel V. Afonine
3Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Malgorzata Biczysko
1International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
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  • For correspondence: biczysko@i.shu.edu.cn
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Abstract

Electron cryo-microscopy (cryo-EM) is fast becoming a major competitor to X-ray crystallography especially for large structures that are difficult or impossible to crystallize. While recent spectacular technology improvements are leading to significantly higher resolution of three-dimensional reconstructions, the average quality of cryo-EM maps is still on the low-resolution end of the range compared to crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here we demonstrate how including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinements of an example structure (chain A of 3j63). The robustness of the procedure is tested for additional structures with up to 7k atoms (3a5x, and chain C of 5fn5) by means of the less expensive semi-empirical (GFN1-xTB) model. Necessary algorithms enabling real-space quantum refinement are implemented in the latest version of qr.refine and are described herein.

Synopsis The implementation of quantum-based real-space refinement in qr.refine is described.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 28, 2020.
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Real-space quantum-based refinement for cryo-EM: Q|R#3
Lum Wang, Holger Kruse, Oleg V. Sobolev, Nigel W. Moriarty, Mark P. Waller, Pavel V. Afonine, Malgorzata Biczysko
bioRxiv 2020.05.25.115386; doi: https://doi.org/10.1101/2020.05.25.115386
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Real-space quantum-based refinement for cryo-EM: Q|R#3
Lum Wang, Holger Kruse, Oleg V. Sobolev, Nigel W. Moriarty, Mark P. Waller, Pavel V. Afonine, Malgorzata Biczysko
bioRxiv 2020.05.25.115386; doi: https://doi.org/10.1101/2020.05.25.115386

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