Analysis of phases in the structure determination of an
icosahedral virus

J 2011

Analysis of phases in the structure determination of an icosahedral virus

PLEVKA, Pavel, Barbel KAUFMANN and Michael G. ROSSMANN

Basic information

Original name

Analysis of phases in the structure determination of an icosahedral virus

Authors

PLEVKA, Pavel, Barbel KAUFMANN and Michael G. ROSSMANN

Edition

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, HOBOKEN, WILEY-BLACKWELL, 2011, 0907-4449

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 12.619

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1107/S090744491101448X

UT WoS

000291212900009

Keywords in English

phase extension; molecular replacement; icosahedral averaging; noncrystallographic symmetry

Abstract

V originále

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or pi. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed.

Citovat

PLEVKA, Pavel, Barbel KAUFMANN and Michael G. ROSSMANN. Analysis of phases in the structure determination of an icosahedral virus. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY. HOBOKEN: WILEY-BLACKWELL, 2011, vol. 67, June, p. 568-577. ISSN 0907-4449. Available from: https://dx.doi.org/10.1107/S090744491101448X.

@article{1376817,
   author = {Plevka, Pavel and Kaufmann, Barbel and Rossmann, Michael G.},
   article_location = {HOBOKEN},
   article_number = {June},
   doi = {http://dx.doi.org/10.1107/S090744491101448X},
   keywords = {phase extension; molecular replacement; icosahedral averaging; noncrystallographic symmetry},
   language = {eng},
   issn = {0907-4449},
   journal = {ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY},
   title = {Analysis of phases in the structure determination of an icosahedral virus},
   volume = {67},
   year = {2011}
}

TY  - JOUR
ID  - 1376817
AU  - Plevka, Pavel - Kaufmann, Barbel - Rossmann, Michael G.
PY  - 2011
TI  - Analysis of phases in the structure determination of an icosahedral virus
JF  - ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
VL  - 67
IS  - June
SP  - 568-577
EP  - 568-577
PB  - WILEY-BLACKWELL
SN  - 09074449
KW  - phase extension
KW  - molecular replacement
KW  - icosahedral averaging
KW  - noncrystallographic symmetry
N2  - The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or pi. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed.
ER  -

PLEVKA, Pavel, Barbel KAUFMANN and Michael G. ROSSMANN. Analysis of phases in the structure determination of an icosahedral virus. \textit{ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY}. HOBOKEN: WILEY-BLACKWELL, 2011, vol.~67, June, p.~568-577. ISSN~0907-4449. Available from: https://dx.doi.org/10.1107/S090744491101448X.

Detailed Information on Publication Record