Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal
Abstract
A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilligeret al.(2016),Acta Cryst.D72, 346–358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. Thephenix.plan_sad_experimenttool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. Thephenix.scale_and_mergetool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and thephenix.anomalous_signaltool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing.
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Univ. of Cambridge (United Kingdom)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Michigan, Ann Arbor, MI (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- National Institutes of Health (NIH); USDOE Office of Science (SC)
- OSTI Identifier:
- 1254848
- Alternate Identifier(s):
- OSTI ID: 1378774
- Report Number(s):
- LA-UR-15-22792
Journal ID: ISSN 2059-7983; ACSDAD; PII: S2059798315019403
- Grant/Contract Number:
- AC52-06NA25396; AC02-05CH11231; P01GM063210; P01AI055672
- Resource Type:
- 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; SAD phasing; anomalous signal; experimental design
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? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. United States: N. p., 2016.
Web. doi:10.1107/S2059798315019403.
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? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. United States. https://doi.org/10.1107/S2059798315019403
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? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal". United States. https://doi.org/10.1107/S2059798315019403. https://www.osti.gov/servlets/purl/1254848.
@article{osti_1254848,
title = {Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal},
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. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilligeret al.(2016),Acta Cryst.D72, 346–358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. Thephenix.plan_sad_experimenttool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. Thephenix.scale_and_mergetool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and thephenix.anomalous_signaltool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing.},
doi = {10.1107/S2059798315019403},
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}
}
Web of Science
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