CERES : a cryo-EM re-refinement system for continuous improvement of deposited models

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; Poon, Billy K.; Chen, Vincent B.; Adams, Paul D.

doi:10.1107/S2059798320015879

Title: CERES : a cryo-EM re-refinement system for continuous improvement of deposited models

Journal Article · Fri Jan 01 00:00:00 EST 2021 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798320015879· OSTI ID:1737714

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The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System ( CERES ) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231.; AC02-05CH11231; 5P01GM063210

OSTI ID:: 1737714

Alternate ID(s):: OSTI ID: 1766536

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Vol. 77 Journal Issue: 1; ISSN 2059-7983

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

Country of Publication:: United Kingdom

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Title: CERES : a cryo-EM re-refinement system for continuous improvement of deposited models

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References (53)

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