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

Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

Benjamin A Barad, Nathaniel Echols, Ray Y-R Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser
doi: https://doi.org/10.1101/014738
Benjamin A Barad
1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA USA
2Graduate Group in Biophysics, University of California, San Francisco, CA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nathaniel Echols
3Lawrence Berkeley National Laboratory, Berkeley, CA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ray Y-R Wang
4Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, WA USA
5Department of Biochemistry, University of Washington, Seattle, WA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yifan Cheng
6Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Frank DiMaio
5Department of Biochemistry, University of Washington, Seattle, WA USA
7Institute for Protein Design, Seattle, WA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul D Adams
3Lawrence Berkeley National Laboratory, Berkeley, CA USA
8Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James S Fraser
1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Advances in electron cryomicroscopy allow for the building of de novo atomic models into high resolution Coulomb potential maps. While established validation metrics independently assess map quality and model geometry, methods to assess the precise fitting of an atomic model into the map and to validate the interpretation of high resolution features are less well developed. Here, we present EMRinger, which tests model-to-map agreement using side-chain dihedral-directed map density measurements. These measurements reveal local map density peaks and show that peaks located at rotameric angles are a sensitive marker of whether the backbone is correctly positioned. The EMRinger Score can be improved by model refinement, suggesting its utility as an effective model-to-map validation metric. Additionally, EMRinger sampling identifies how radiation damage alters scattering from negatively charged amino acids during data collection. EMRinger will be useful in assessing how advances in cryo-EM increase the ability to resolve and model high-resolution features.

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-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted February 03, 2015.
Download PDF

Supplementary Material

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.
Side-chain-directed model and map validation for 3D Electron Cryomicroscopy
(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
Side-chain-directed model and map validation for 3D Electron Cryomicroscopy
Benjamin A Barad, Nathaniel Echols, Ray Y-R Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser
bioRxiv 014738; doi: https://doi.org/10.1101/014738
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Side-chain-directed model and map validation for 3D Electron Cryomicroscopy
Benjamin A Barad, Nathaniel Echols, Ray Y-R Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser
bioRxiv 014738; doi: https://doi.org/10.1101/014738

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

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4239)
  • Biochemistry (9171)
  • Bioengineering (6804)
  • Bioinformatics (24062)
  • Biophysics (12154)
  • Cancer Biology (9564)
  • Cell Biology (13824)
  • 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 (49107)
  • 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)