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

Journal Article · · Nature Methods
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)
+ Show Author Affiliations

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.

Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
National Inst. of Health; USDOE Office of Science (SC)
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
1604578
Journal Information:
Nature Methods, Journal Name: Nature Methods Journal Issue: 3 Vol. 17; ISSN 1548-7091
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (3)

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution journal December 2019
Structural basis for strand-transfer inhibitor binding to HIV intasomes journal January 2020
Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes journal January 2020

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