Format

Send to

Choose Destination
Nat Methods. 2020 Mar;17(3):328-334. doi: 10.1038/s41592-020-0731-1. Epub 2020 Feb 10.

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

Author information

1
Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA. gregp@slac.stanford.edu.
2
Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
3
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
4
Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA. wahc@stanford.edu.
5
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA. wahc@stanford.edu.

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.

PMID:
32042190
DOI:
10.1038/s41592-020-0731-1

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center