A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.; Sobolev, Oleg V.

doi:10.1038/s41592-018-0173-1

Title: A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

Journal Article · 29 October 2018 · Nature Methods

DOI: https://doi.org/10.1038/s41592-018-0173-1 · OSTI ID:1601815

^[1]; Adams, Paul D. ^[2]; Afonine, Pavel V. ^[3];

^[4]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium, Los Alamos, NM (United States
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics & Integrated Bioimaging Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics & Integrated Bioimaging Division; Shanghai Univ., Shanghai (China). Dept. of Physics and International Centre for Quantum and Molecular Structures
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics & Integrated Bioimaging Division

Here, we report a fully automated procedure for the optimization and interpretation of reconstructions from cryo-electron microscopy (cryo-EM) data, available in Phenix as phenix.map_to_model. We applied our approach to 476 datasets with resolution of 4.5 Å or better, including reconstructions of 47 ribosomes and 32 other protein–RNA complexes. The median fraction of residues in the deposited structures reproduced automatically was 71% for reconstructions determined at resolutions of 3 Å or better and 47% for those at resolutions worse than 3 Å.

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

Sponsoring Organization:: National Institutes of Health (NIH); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC)

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

OSTI ID:: 1601815

Report Number(s):: LA-UR-18-20450; ark:/13030/qt7tv065s4

Journal Information:: Nature Methods, Journal Name: Nature Methods Journal Issue: 11 Vol. 15; ISSN 1548-7091

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution Zhang, Kaiming; Li, Shanshan; Kappel, Kalli Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13494-7	journal	December 2019
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