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Title: EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

Abstract

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

Authors:
ORCiD logo [1];  [2];  [3];  [1];  [4];  [5]; ORCiD logo [6]
  1. Univ. of California, San Francisco, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of Washington, Seattle, WA (United States)
  4. Univ. of Washington, Seattle, WA (United States); Institute for Protein Design, Seattle, WA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  6. Univ. of California, San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1257854
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 12; Journal Issue: 10; Journal ID: ISSN 1548-7091
Country of Publication:
United States
Language:
English
Subject:
47 OTHER INSTRUMENTATION

Citation Formats

Barad, Benjamin A., Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D., and Fraser, James S. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy. United States: N. p., 2015. Web. doi:10.1038/nmeth.3541.
Barad, Benjamin A., Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D., & Fraser, James S. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy. United States. doi:10.1038/nmeth.3541.
Barad, Benjamin A., Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D., and Fraser, James S. Mon . "EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy". United States. doi:10.1038/nmeth.3541. https://www.osti.gov/servlets/purl/1257854.
@article{osti_1257854,
title = {EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy},
author = {Barad, Benjamin A. and Echols, Nathaniel and Wang, Ray Yu-Ruei and Cheng, Yifan and DiMaio, Frank and Adams, Paul D. and Fraser, James S.},
abstractNote = {Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.},
doi = {10.1038/nmeth.3541},
journal = {Nature Methods},
issn = {1548-7091},
number = 10,
volume = 12,
place = {United States},
year = {2015},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 43 works
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