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Title: Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing

Abstract

A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. We present a simple theoretical framework for describing measurements of anomalous differences and the resulting useful anomalous correlation and anomalous signal in a SAD experiment. Here, the useful anomalous correlation is defined as the correlation of anomalous differences with ideal anomalous differences from the anomalous substructure. The useful anomalous correlation reflects the accuracy of the data and the absence of minor sites. The useful anomalous correlation also reflects the information available for estimating crystallographic phases once the substructure has been determined. In contrast, the anomalous signal (the peak height in a model-phased anomalous difference Fourier at the coordinates of atoms in the anomalous substructure) reflects the information available about each site in the substructure and is related to the ability to find the substructure. A theoretical analysis shows that the expected value of the anomalous signal is the product of the useful anomalous correlation, the square root of the ratio of the number of unique reflections in the data set to the number of sites in the substructure, and a function that decreases with increasing values of the atomic displacement factormore » for the atoms in the substructure. In conclusion, this means that the ability to find the substructure in a SAD experiment is increased by high data quality and by a high ratio of reflections to sites in the substructure, and is decreased by high atomic displacement factors for the substructure.« less

Authors:
 [1];  [2];  [1];  [3];  [4];  [4];  [3]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Univ. of Cambridge (United Kingdom)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Univ. of Michigan, Ann Arbor, MI (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
National Institutes of Health (NIH); USDOE Office of Science (SC)
OSTI Identifier:
1254849
Alternate Identifier(s):
OSTI ID: 1378754
Report Number(s):
LA-UR-15-22794
Journal ID: ISSN 2059-7983; ACSDAD
Grant/Contract Number:  
AC52-06NA25396; AC02-05CH11231; P01GM063210; P01AI055672
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 72; Journal Issue: 3; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science; SAD phasing; anomalous signal; anomalous phasing; solving structures

Citation Formats

Terwilliger, Thomas C., Bunkóczi, Gábor, Hung, Li-Wei, Zwart, Peter H., Smith, Janet L., Akey, David L., and Adams, Paul D.. Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. United States: N. p., 2016. Web. doi:10.1107/S2059798315019269.
Terwilliger, Thomas C., Bunkóczi, Gábor, Hung, Li-Wei, Zwart, Peter H., Smith, Janet L., Akey, David L., & Adams, Paul D.. Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. United States. doi:10.1107/S2059798315019269.
Terwilliger, Thomas C., Bunkóczi, Gábor, Hung, Li-Wei, Zwart, Peter H., Smith, Janet L., Akey, David L., and Adams, Paul D.. Tue . "Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing". United States. doi:10.1107/S2059798315019269. https://www.osti.gov/servlets/purl/1254849.
@article{osti_1254849,
title = {Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing},
author = {Terwilliger, Thomas C. and Bunkóczi, Gábor and Hung, Li-Wei and Zwart, Peter H. and Smith, Janet L. and Akey, David L. and Adams, Paul D.},
abstractNote = {A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. We present a simple theoretical framework for describing measurements of anomalous differences and the resulting useful anomalous correlation and anomalous signal in a SAD experiment. Here, the useful anomalous correlation is defined as the correlation of anomalous differences with ideal anomalous differences from the anomalous substructure. The useful anomalous correlation reflects the accuracy of the data and the absence of minor sites. The useful anomalous correlation also reflects the information available for estimating crystallographic phases once the substructure has been determined. In contrast, the anomalous signal (the peak height in a model-phased anomalous difference Fourier at the coordinates of atoms in the anomalous substructure) reflects the information available about each site in the substructure and is related to the ability to find the substructure. A theoretical analysis shows that the expected value of the anomalous signal is the product of the useful anomalous correlation, the square root of the ratio of the number of unique reflections in the data set to the number of sites in the substructure, and a function that decreases with increasing values of the atomic displacement factor for the atoms in the substructure. In conclusion, this means that the ability to find the substructure in a SAD experiment is increased by high data quality and by a high ratio of reflections to sites in the substructure, and is decreased by high atomic displacement factors for the substructure.},
doi = {10.1107/S2059798315019269},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 3,
volume = 72,
place = {United States},
year = {Tue Mar 01 00:00:00 EST 2016},
month = {Tue Mar 01 00:00:00 EST 2016}
}

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Works referenced in this record:

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