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Title: Measurement of atom resolvability in cryo-EM maps with Q-scores

Abstract

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.


Citation Formats

Pintilie, Grigore, Zhang, Kaiming, Su, Zhaoming, Li, Shanshan, Schmid, Michael F., and Chiu, Wah. Measurement of atom resolvability in cryo-EM maps with Q-scores. United States: N. p., 2020. Web. doi:10.1038/s41592-020-0731-1.
Pintilie, Grigore, Zhang, Kaiming, Su, Zhaoming, Li, Shanshan, Schmid, Michael F., & Chiu, Wah. Measurement of atom resolvability in cryo-EM maps with Q-scores. United States. doi:10.1038/s41592-020-0731-1.
Pintilie, Grigore, Zhang, Kaiming, Su, Zhaoming, Li, Shanshan, Schmid, Michael F., and Chiu, Wah. Mon . "Measurement of atom resolvability in cryo-EM maps with Q-scores". United States. doi:10.1038/s41592-020-0731-1.
@article{osti_1604578,
title = {Measurement of atom resolvability in cryo-EM maps with Q-scores},
author = {Pintilie, Grigore and Zhang, Kaiming and Su, Zhaoming and Li, Shanshan and Schmid, Michael F. and Chiu, Wah},
abstractNote = {Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.},
doi = {10.1038/s41592-020-0731-1},
journal = {Nature Methods},
number = [3],
volume = [17],
place = {United States},
year = {2020},
month = {2}
}

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Works referenced in this record:

Quantifying the local resolution of cryo-EM density maps
journal, November 2013

  • Kucukelbir, Alp; Sigworth, Fred J.; Tagare, Hemant D.
  • Nature Methods, Vol. 11, Issue 1
  • DOI: 10.1038/nmeth.2727

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018


Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy
journal, July 2017

  • Joseph, Agnel Praveen; Lagerstedt, Ingvar; Patwardhan, Ardan
  • Journal of Structural Biology, Vol. 199, Issue 1
  • DOI: 10.1016/j.jsb.2017.05.007

Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018

  • Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/S2059798318006551

Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment
journal, May 2016


Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage
journal, February 2016

  • Pintilie, Grigore; Chen, Dong-Hua; Haase-Pettingell, Cameron A.
  • Biophysical Journal, Vol. 110, Issue 4
  • DOI: 10.1016/j.bpj.2015.11.3522

Cryo-EM model validation using independent map reconstructions: Cryo-EM Model Validation
journal, May 2013

  • DiMaio, Frank; Zhang, Junjie; Chiu, Wah
  • Protein Science, Vol. 22, Issue 6
  • DOI: 10.1002/pro.2267

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
journal, October 2009


Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
journal, September 2009

  • DiMaio, Frank; Tyka, Michael D.; Baker, Matthew L.
  • Journal of Molecular Biology, Vol. 392, Issue 1
  • DOI: 10.1016/j.jmb.2009.07.008

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
journal, August 2015

  • Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei
  • Nature Methods, Vol. 12, Issue 10
  • DOI: 10.1038/nmeth.3541

Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores
journal, December 2018


New tools for automated high-resolution cryo-EM structure determination in RELION-3
journal, November 2018

  • Zivanov, Jasenko; Nakane, Takanori; Forsberg, Björn O.
  • eLife, Vol. 7
  • DOI: 10.7554/eLife.42166

Interpretation of atomic displacement parameters from diffraction studies of crystals
journal, February 1988

  • Dunitz, Jack D.; Schomaker, Verner; Trueblood, Kenneth N.
  • The Journal of Physical Chemistry, Vol. 92, Issue 4
  • DOI: 10.1021/j100315a002

Atomic Dispacement Parameter Nomenclature. Report of a Subcommittee on Atomic Displacement Parameter Nomenclature
journal, September 1996

  • Trueblood, K. N.; Bürgi, H. B.; Burzlaff, H.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 52, Issue 5
  • DOI: 10.1107/S0108767396005697

How large B-factors can be in protein crystal structures
journal, February 2018


Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

  • Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
  • DOI: 10.1073/pnas.1621152114

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
journal, July 2016


Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures
journal, October 2017

  • Meyder, Agnes; Nittinger, Eva; Lange, Gudrun
  • Journal of Chemical Information and Modeling, Vol. 57, Issue 10
  • DOI: 10.1021/acs.jcim.7b00391

A beginner's guide to radiation damage
journal, February 2009


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
journal, February 2017

  • Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul
  • Nature Methods, Vol. 14, Issue 4
  • DOI: 10.1038/nmeth.4193

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084