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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 (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.

Authors:
ORCiD logo; ORCiD logo; ; ; ; ; ORCiD logo; ORCiD logo; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Laboratory (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:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Volume: 74 Journal Issue: 11; Journal ID: ISSN 2059-7983
Publisher:
International Union of Crystallography (IUCr)
Country of Publication:
United Kingdom
Language:
English
Subject:
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; neutron crystallography; integration; profile fitting

Citation Formats

Sullivan, Brendan, Archibald, Rick, Langan, Patricia S., Dobbek, Holger, Bommer, Martin, McFeeters, Robert L., Coates, Leighton, Wang, Xiaoping, Gallmeier, Franz, Carpenter, John M., Lynch, Vickie, and Langan, Paul. Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. United Kingdom: N. p., 2018. Web. doi:10.1107/S2059798318013347.
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Sullivan, Brendan, Archibald, Rick, Langan, Patricia S., Dobbek, Holger, Bommer, Martin, McFeeters, Robert L., Coates, Leighton, Wang, Xiaoping, Gallmeier, Franz, Carpenter, John M., Lynch, Vickie, & Langan, Paul. Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. United Kingdom. https://doi.org/10.1107/S2059798318013347
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Sullivan, Brendan, Archibald, Rick, Langan, Patricia S., Dobbek, Holger, Bommer, Martin, McFeeters, Robert L., Coates, Leighton, Wang, Xiaoping, Gallmeier, Franz, Carpenter, John M., Lynch, Vickie, 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 Kingdom. https://doi.org/10.1107/S2059798318013347.
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@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 and Archibald, Rick and Langan, Patricia S. and Dobbek, Holger and Bommer, Martin and McFeeters, Robert L. and Coates, Leighton and Wang, Xiaoping and Gallmeier, Franz and Carpenter, John M. and Lynch, Vickie 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},
number = 11,
volume = 74,
place = {United Kingdom},
year = {Mon Oct 29 00:00:00 EDT 2018},
month = {Mon Oct 29 00:00:00 EDT 2018}
}
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https://doi.org/10.1107/S2059798318013347
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