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Title: New tools for the analysis and validation of cryo-EM maps and atomic models

Abstract

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d 99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.

Authors:
ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo;
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
National Institutes of Health (NIH); Centre National de la Recherche Scientifique (CNRS); Association pour la Recherche sur le Cancer (ARC); Institut National du Cancer (INCa); Agence National pour la Recherche (ANR); European Strategy Forum on Research Infrastructures (ESFRI); USDOE Office of Science (SC)
OSTI Identifier:
1468375
Alternate Identifier(s):
OSTI ID: 1471356; OSTI ID: 1477375
Report Number(s):
LA-UR-17-31128
Journal ID: ISSN 2059-7983; ACSDAD; PII: S2059798318009324
Grant/Contract Number:  
AC02-05CH11231; AC52-06NA25396; GM063210
Resource Type:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Volume: 74 Journal Issue: 9; Journal ID: ISSN 2059-7983
Publisher:
International Union of Crystallography (IUCr)
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biological Science

Citation Formats

Afonine, Pavel V., Klaholz, Bruno P., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas C., Adams, Paul D., and Urzhumtsev, Alexandre. New tools for the analysis and validation of cryo-EM maps and atomic models. United Kingdom: N. p., 2018. Web. doi:10.1107/S2059798318009324.
Afonine, Pavel V., Klaholz, Bruno P., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas C., Adams, Paul D., & Urzhumtsev, Alexandre. New tools for the analysis and validation of cryo-EM maps and atomic models. United Kingdom. doi:10.1107/S2059798318009324.
Afonine, Pavel V., Klaholz, Bruno P., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas C., Adams, Paul D., and Urzhumtsev, Alexandre. Mon . "New tools for the analysis and validation of cryo-EM maps and atomic models". United Kingdom. doi:10.1107/S2059798318009324.
@article{osti_1468375,
title = {New tools for the analysis and validation of cryo-EM maps and atomic models},
author = {Afonine, Pavel V. and Klaholz, Bruno P. and Moriarty, Nigel W. and Poon, Billy K. and Sobolev, Oleg V. and Terwilliger, Thomas C. and Adams, Paul D. and Urzhumtsev, Alexandre},
abstractNote = {Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d 99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.},
doi = {10.1107/S2059798318009324},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 9,
volume = 74,
place = {United Kingdom},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1107/S2059798318009324

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Cited by: 29 works
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