Journal
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
Volume 74, Issue -, Pages 814-840Publisher
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S2059798318009324
Keywords
cryo-EM; atomic models; model quality; data quality; validation; resolution
Funding
- NIH [GM063210]
- PHENIX Industrial Consortium
- US Department of Energy [DE-AC02-05CH11231]
- French Infrastructure for Integrated Structural Biology (FRISBI) [ANR-10-INSB-05-01]
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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.
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