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:
-
[1];
[6]
- Univ. of California, San Francisco, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Washington, Seattle, WA (United States)
- Univ. of Washington, Seattle, WA (United States); Institute for Protein Design, Seattle, WA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
- Univ. of California, San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1257854
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- 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. https://doi.org/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. https://doi.org/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},
number = 10,
volume = 12,
place = {United States},
year = {Mon Aug 17 00:00:00 EDT 2015},
month = {Mon Aug 17 00:00:00 EDT 2015}
}
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