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Title: New tools for the analysis and validation of cryo-EM maps and atomic models

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_sharpento improve maps andphenix.mtriageto 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. Lastly, the application of these tools to deposited cryo-EM atomic models and maps is also presented.
Authors:
ORCiD logo [1] ; ORCiD logo [2] ; ORCiD logo [3] ; ORCiD logo [3] ; ORCiD logo [3] ; ORCiD logo [4] ; ORCiD logo [5] ;  [6]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Shanghai Univ., Shanghai (China)
  2. Inst. of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch (France)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mexico Consortium, Los Alamos, NM (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
  6. Inst. of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch (France); Univ. de Lorraine, Vandoeuvre-les-Nancy (France)
Publication Date:
Report Number(s):
LA-UR-17-31128
Journal ID: ISSN 2059-7983; ACSDAD
Grant/Contract Number:
AC52-06NA25396; GM063210; AC02-05CH11231
Type:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 74; Journal Issue: 9; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Research Org:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
National Institutes of Health (NIH); Centre National de la Recherche Scientifique (CNRS); Association pour la Recherche sur le Cancer (ARC); Institut National du Cancer (INCa); Agence National pour la Recherche (ANR); European Strategy Forum on Research Infrastructures (ESFRI); USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; cryo-EM; atomic models; model quality; data quality; validation; resolution
OSTI Identifier:
1468375
Alternate Identifier(s):
OSTI ID: 1471356; OSTI ID: 1477375

Afonine, Pavel V., Klaholz, Bruno P., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas C., Adams, Paul D., and Urzhumtsev, Alexandre. New tools for the analysis and validation of cryo-EM maps and atomic models. United States: N. p., Web. doi:10.1107/S2059798318009324.
Afonine, Pavel V., Klaholz, Bruno P., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas C., Adams, Paul D., & Urzhumtsev, Alexandre. New tools for the analysis and validation of cryo-EM maps and atomic models. United States. doi:10.1107/S2059798318009324.
Afonine, Pavel V., Klaholz, Bruno P., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas C., Adams, Paul D., and Urzhumtsev, Alexandre. 2018. "New tools for the analysis and validation of cryo-EM maps and atomic models". United States. doi:10.1107/S2059798318009324.
@article{osti_1468375,
title = {New tools for the analysis and validation of cryo-EM maps and atomic models},
author = {Afonine, Pavel V. and Klaholz, Bruno P. and Moriarty, Nigel W. and Poon, Billy K. and Sobolev, Oleg V. and Terwilliger, Thomas C. and Adams, Paul D. and Urzhumtsev, Alexandre},
abstractNote = {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 d99 to estimate resolution, phenix.auto_sharpento improve maps andphenix.mtriageto 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. Lastly, the application of these tools to deposited cryo-EM atomic models and maps is also presented.},
doi = {10.1107/S2059798318009324},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 9,
volume = 74,
place = {United States},
year = {2018},
month = {9}
}

Works referenced in this record:

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
  • Adams, Paul D.; Afonine, Pavel V.; Bunk�czi, G�bor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Improved methods for building protein models in electron density maps and the location of errors in these models
journal, March 1991
  • Jones, T. A.; Zou, J. Y.; Cowan, S. W.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 2, p. 110-119
  • DOI: 10.1107/S0108767390010224