Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Measurement of Atom Resolvability in CryoEM Maps with Q-scores

View ORCID ProfileGrigore Pintilie, Kaiming Zhang, Zhaoming Su, Shanshan Li, Michael F. Schmid, Wah Chiu
doi: https://doi.org/10.1101/722991
Grigore Pintilie
1Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Grigore Pintilie
  • For correspondence: gregp@slac.stanford.edu wahc@stanford.edu
Kaiming Zhang
1Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zhaoming Su
1Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shanshan Li
1Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael F. Schmid
2Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wah Chiu
1Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
2Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: gregp@slac.stanford.edu wahc@stanford.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

CryoEM density 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 cryoEM 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 cryoEM 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 cryoEM maps for both protein and RNA. Assuming the models they are calculated from are well-fitted to the map, Q-scores can thus be used as another measure to indicate resolvability of features in cryoEM maps at various scales, from entire complexes down to individual atoms. Q-score analysis of multiple cryoEM maps of the same proteins derived from different labs confirms reproducibility of structural features down to water and ion atoms.

Footnotes

  • https://cryoem.slac.stanford.edu/ncmi/resources/software/mapq

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted August 05, 2019.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Measurement of Atom Resolvability in CryoEM Maps with Q-scores
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Measurement of Atom Resolvability in CryoEM Maps with Q-scores
Grigore Pintilie, Kaiming Zhang, Zhaoming Su, Shanshan Li, Michael F. Schmid, Wah Chiu
bioRxiv 722991; doi: https://doi.org/10.1101/722991
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Measurement of Atom Resolvability in CryoEM Maps with Q-scores
Grigore Pintilie, Kaiming Zhang, Zhaoming Su, Shanshan Li, Michael F. Schmid, Wah Chiu
bioRxiv 722991; doi: https://doi.org/10.1101/722991

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biochemistry
Subject Areas
All Articles
  • Animal Behavior and Cognition (4239)
  • Biochemistry (9171)
  • Bioengineering (6804)
  • Bioinformatics (24062)
  • Biophysics (12154)
  • Cancer Biology (9564)
  • Cell Biology (13825)
  • Clinical Trials (138)
  • Developmental Biology (7656)
  • Ecology (11736)
  • Epidemiology (2066)
  • Evolutionary Biology (15540)
  • Genetics (10670)
  • Genomics (14358)
  • Immunology (9511)
  • Microbiology (22901)
  • Molecular Biology (9129)
  • Neuroscience (49112)
  • Paleontology (357)
  • Pathology (1487)
  • Pharmacology and Toxicology (2583)
  • Physiology (3851)
  • Plant Biology (8351)
  • Scientific Communication and Education (1473)
  • Synthetic Biology (2301)
  • Systems Biology (6205)
  • Zoology (1302)