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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. Here, 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.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]
  1. Stanford Univ., CA (United States)
  2. SLAC National Accelerator Lab., Stanford Univ., Menlo Park, CA (United States)
  3. Stanford Univ., CA (United States); SLAC National Accelerator Lab., Stanford Univ., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Inst. of Health
OSTI Identifier:
1604578
Grant/Contract Number:  
AC02-76SF00515; R01GM079429; P41GM103832; S10OD021600
Resource Type:
Accepted Manuscript
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 17; Journal Issue: 3; Journal ID: ISSN 1548-7091
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

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:https://doi.org/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:https://doi.org/10.1038/s41592-020-0731-1. https://www.osti.gov/servlets/purl/1604578.
@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. Here, 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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