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

Afonine, Pavel V.; Klaholz, Bruno P.; Moriarty, Nigel W.; Poon, Billy K.; Sobolev, Oleg V.; Terwilliger, Thomas C.; Adams, Paul D.; Urzhumtsev, Alexandre

doi:10.1107/S2059798318009324

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

Journal Article · Mon Sep 03 00:00:00 EDT 2018 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798318009324· OSTI ID:1468375

;

; Urzhumtsev, Alexandre

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 d99 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.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: 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), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC52-06NA25396; GM063210

OSTI ID:: 1468375

Alternate ID(s):: OSTI ID: 1471356; OSTI ID: 1477375; OSTI ID: 1881871

Report Number(s):: LA-UR-17-31128; ACSDAD; PII: S2059798318009324

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Vol. 74 Journal Issue: 9; ISSN 2059-7983

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 388 works

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