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Title: Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space

Abstract

Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios. A method has been developed to fit weak data based on three-dimensional profile fitting of Bragg peaks in reciprocal space by an Ikeda–Carpenter function with a bivariate Gaussian. When applied to data collected from three different proteins, three-dimensional profile fitting yields intensities with higher correlation coefficients (CC 1/2) at high resolutions, decreased R free factors, extended resolutions and improved nuclear density maps. Importantly, additional features are revealed in nuclear density maps that may provide additional scientific information. Furthermore, these results suggest that three-dimensional profile fitting will help to extend the capabilities of neutron macromolecular crystallography.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [3];  [4];  [5]; ORCiD logo [1]; ORCiD logo [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lentigen Technology, Gaithersburg, MD (United States)
  3. Humboldt-Univ. zu Berlin, Berlin (Germany)
  4. Humboldt-Univ. zu Berlin, Berlin (Germany); Max Delbruck Center for Molecular Medicine, Berlin (Germany)
  5. Univ. of Alabama in Huntsville, Huntsville, AL (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1479603
Alternate Identifier(s):
OSTI ID: 1496005
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 74; Journal Issue: 11; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United States
Language:
English
Subject:
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; neutron crystallography; integration; profile fitting

Citation Formats

Sullivan, Brendan T., Archibald, Rick K., Langan, Patricia S., Dobbek, Holger, Bommer, Martin, McFeeters, Robert L., Coates, Leighton, Wang, Xiaoping, Gallmeier, Franz X., Carpenter, John M., Lynch, Vickie E., and Langan, Paul. Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. United States: N. p., 2018. Web. doi:10.1107/S2059798318013347.
Sullivan, Brendan T., Archibald, Rick K., Langan, Patricia S., Dobbek, Holger, Bommer, Martin, McFeeters, Robert L., Coates, Leighton, Wang, Xiaoping, Gallmeier, Franz X., Carpenter, John M., Lynch, Vickie E., & Langan, Paul. Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. United States. doi:10.1107/S2059798318013347.
Sullivan, Brendan T., Archibald, Rick K., Langan, Patricia S., Dobbek, Holger, Bommer, Martin, McFeeters, Robert L., Coates, Leighton, Wang, Xiaoping, Gallmeier, Franz X., Carpenter, John M., Lynch, Vickie E., and Langan, Paul. Mon . "Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space". United States. doi:10.1107/S2059798318013347.
@article{osti_1479603,
title = {Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space},
author = {Sullivan, Brendan T. and Archibald, Rick K. and Langan, Patricia S. and Dobbek, Holger and Bommer, Martin and McFeeters, Robert L. and Coates, Leighton and Wang, Xiaoping and Gallmeier, Franz X. and Carpenter, John M. and Lynch, Vickie E. and Langan, Paul},
abstractNote = {Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios. A method has been developed to fit weak data based on three-dimensional profile fitting of Bragg peaks in reciprocal space by an Ikeda–Carpenter function with a bivariate Gaussian. When applied to data collected from three different proteins, three-dimensional profile fitting yields intensities with higher correlation coefficients (CC1/2) at high resolutions, decreased Rfree factors, extended resolutions and improved nuclear density maps. Importantly, additional features are revealed in nuclear density maps that may provide additional scientific information. Furthermore, these results suggest that three-dimensional profile fitting will help to extend the capabilities of neutron macromolecular crystallography.},
doi = {10.1107/S2059798318013347},
journal = {Acta Crystallographica. Section D. Structural Biology},
issn = {2059-7983},
number = 11,
volume = 74,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1107/S2059798318013347

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