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Title: X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

Abstract

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

Authors:
 [1];  [2]; ORCiD logo [3];  [2];  [1]
  1. Montana State Univ., Bozeman, MT (United States)
  2. Univ. of Cambridge (United Kingdom)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1254834
Report Number(s):
LA-UR-14-28194
Journal ID: ISSN 1754-2189; nprot.2015.069
Grant/Contract Number:  
AC52-06NA25396; GM110732; GM108888; EPS-110134
Resource Type:
Accepted Manuscript
Journal Name:
Nature Protocols
Additional Journal Information:
Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 1754-2189
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Jackson, Ryan N., McCoy, Airlie J., Terwilliger, Thomas C., Read, Randy J., and Wiedenheft, Blake. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. United States: N. p., 2015. Web. doi:10.1038/nprot.2015.069.
Jackson, Ryan N., McCoy, Airlie J., Terwilliger, Thomas C., Read, Randy J., & Wiedenheft, Blake. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. United States. doi:10.1038/nprot.2015.069.
Jackson, Ryan N., McCoy, Airlie J., Terwilliger, Thomas C., Read, Randy J., and Wiedenheft, Blake. Thu . "X-ray structure determination using low-resolution electron microscopy maps for molecular replacement". United States. doi:10.1038/nprot.2015.069. https://www.osti.gov/servlets/purl/1254834.
@article{osti_1254834,
title = {X-ray structure determination using low-resolution electron microscopy maps for molecular replacement},
author = {Jackson, Ryan N. and McCoy, Airlie J. and Terwilliger, Thomas C. and Read, Randy J. and Wiedenheft, Blake},
abstractNote = {Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.},
doi = {10.1038/nprot.2015.069},
journal = {Nature Protocols},
number = 9,
volume = 10,
place = {United States},
year = {2015},
month = {7}
}

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