Improving experimental phases for strong reflections prior to density modification
Abstract
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,more »
- Authors:
-
- Univ. of Lubeck, Lubeck (Germany)
- Univ. of Lubeck, Lubeck (Germany); Chinese Academy of Sciences, Shanghai (People's Republic of China)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Univ. of Cambridge, Cambridge (England)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1255151
- Report Number(s):
- LA-UR-15-29209
Journal ID: ISSN 0907-4449; ABCRE6; PII: S0907444913018167
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D: Biological Crystallography
- Additional Journal Information:
- Journal Volume: 69; Journal Issue: 10; Journal ID: ISSN 0907-4449
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; experimental phasing; density modification; genetic algorithms
Citation Formats
Uervirojnangkoorn, Monarin, Hilgenfeld, Rolf, Terwilliger, Thomas C., and Read, Randy J. Improving experimental phases for strong reflections prior to density modification. United States: N. p., 2013.
Web. doi:10.1107/S0907444913018167.
Uervirojnangkoorn, Monarin, Hilgenfeld, Rolf, Terwilliger, Thomas C., & Read, Randy J. Improving experimental phases for strong reflections prior to density modification. United States. https://doi.org/10.1107/S0907444913018167
Uervirojnangkoorn, Monarin, Hilgenfeld, Rolf, Terwilliger, Thomas C., and Read, Randy J. 2013.
"Improving experimental phases for strong reflections prior to density modification". United States. https://doi.org/10.1107/S0907444913018167. https://www.osti.gov/servlets/purl/1255151.
@article{osti_1255151,
title = {Improving experimental phases for strong reflections prior to density modification},
author = {Uervirojnangkoorn, Monarin and Hilgenfeld, Rolf and Terwilliger, Thomas C. and Read, Randy J.},
abstractNote = {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.},
doi = {10.1107/S0907444913018167},
url = {https://www.osti.gov/biblio/1255151},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
issn = {0907-4449},
number = 10,
volume = 69,
place = {United States},
year = {Fri Sep 20 00:00:00 EDT 2013},
month = {Fri Sep 20 00:00:00 EDT 2013}
}
Web of Science
Works referenced in this record:
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
The treatment of errors in the isomorphous replacement method
journal, October 1959
- Blow, D. M.; Crick, F. H. C.
- Acta Crystallographica, Vol. 12, Issue 10
GEST : a program for structure determination from powder diffraction data using a genetic algorithm
journal, May 2007
- Feng, Zhen Jie; Dong, Cheng
- Journal of Applied Crystallography, Vol. 40, Issue 3
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering
journal, January 2009
- Franke, Daniel; Svergun, Dmitri I.
- Journal of Applied Crystallography, Vol. 42, Issue 2, p. 342-346
The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002
- Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
- Journal of Applied Crystallography, Vol. 35, Issue 1
Developments in genetic algorithm techniques for structure solution from powder diffraction data
journal, January 2004
- Harris, Kenneth D. M.; Habershon, Scott; Cheung, Eugene Y.
- Zeitschrift für Kristallographie - Crystalline Materials, Vol. 219, Issue 12
Representation of phase probability distributions for simplified combination of independent phase information
journal, February 1970
- Hendrickson, W. A.; Lattman, E. E.
- Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 26, Issue 2
Finding crystal structures of peptides by random search and evolutionary algorithms
journal, August 2009
- Immirzi, Attilio; Erra, Loredana; Tedesco, Consiglia
- Journal of Applied Crystallography, Vol. 42, Issue 5
Mean phase error and the map-correlation coefficient
journal, November 1993
- Lunin, V. Yu.; Woolfson, M. M.
- Acta Crystallographica Section D Biological Crystallography, Vol. 49, Issue 6
Simple algorithm for a maximum-likelihood SAD function
journal, June 2004
- McCoy, Airlie J.; Storoni, Laurent C.; Read, Randy J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 7
A Genetic Algorithm for the Ab Initio Phasing of Icosahedral Viruses
journal, March 1996
- Miller, S. T.; Hogle, J. M.; Filman, D. J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 52, Issue 2
Use of matrix direct methods for low-resolution phase extension for tRNA
journal, July 1977
- Podjarny, A. D.; Yonath, A.
- Acta Crystallographica Section A, Vol. 33, Issue 4
Improved Fourier coefficients for maps using phases from partial structures with errors
journal, May 1986
- Read, R. J.
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 42, Issue 3
Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution
journal, March 1997
- Shamoo, Y.; Krueger, U.; Rice, L. M.
- Nature Structural Biology, Vol. 4, Issue 3
Crystal structure determination from powder diffraction data by the application of a genetic algorithm
journal, January 1997
- Shankland, K.; David, W. I. F.; Csoka, T.
- Zeitschrift für Kristallographie - Crystalline Materials, Vol. 212, Issue 8
Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.
journal, March 1994
- Skinner, M. M.; Zhang, H.; Leschnitzer, D. H.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 6
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
journal, May 2009
- Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6
Improving experimental phasing: the role of strongest reflections
journal, June 2005
- Vekhter, Yanina
- Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 7
An evolutionary computational approach to the phase problem in macromolecular X-ray crystallography
journal, April 2001
- Webster, Gordon; Hilgenfeld, Rolf
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 57, Issue 3
Structural Insights into Group II Intron Catalysis and Branch-Site Selection
journal, February 2002
- Zhang, L.
- Science, Vol. 295, Issue 5562
Solving the Sayre equations for centrosymmetric structures with a genetic algorithm
journal, June 2004
- Zhou, Yi; Su, Wu-Pei
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 60, Issue 4
Works referencing / citing this record:
Mask-based approach to phasing of single-particle diffraction data
journal, January 2016
- Lunin, Vladimir Y.; Lunina, Natalia L.; Petrova, Tatiana E.
- Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1
Long-wavelength Mesh&Collect native SAD phasing from microcrystals
journal, February 2019
- Cianci, Michele; Nanao, Max; Schneider, Thomas R.
- Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 2
Merging of synchrotron serial crystallographic data by a genetic algorithm
text, January 2016
- Zander, Ulrich; Cianci, Michele; Foos, Nicolas
- Deutsches Elektronen-Synchrotron, DESY, Hamburg
Long-wavelength Mesh&Collect native SAD phasing from microcrystals
text, January 2019
- Cianci, Michele; Nanao, Max; Schneider, Thomas R.
- Deutsches Elektronen-Synchrotron, DESY, Hamburg