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Title: Improving experimental phases for strong reflections prior to density modification

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography
 [1];  [2];  [3];  [4]
  1. Univ. of Lubeck, Lubeck (Germany)
  2. Univ. of Lubeck, Lubeck (Germany); Chinese Academy of Sciences, Shanghai (People's Republic of China)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Univ. of Cambridge, Cambridge (England)
+ Show Author Affiliations

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program,SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.

Research Organization:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1255151
Report Number(s):
LA-UR-15-29209; ABCRE6; PII: S0907444913018167
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography, Vol. 69, Issue 10; ISSN 0907-4449
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

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Cited By (4)

Mask-based approach to phasing of single-particle diffraction data journal January 2016
Long-wavelength Mesh&Collect native SAD phasing from microcrystals journal February 2019
Merging of synchrotron serial crystallographic data by a genetic algorithm text January 2016
Long-wavelength Mesh&Collect native SAD phasing from microcrystals text January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
experimental phasing
density modification
genetic algorithms