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Overcoming the false-minima problem in direct methods: Structure determination of the packaging enzyme P4 from bacteriophage f13

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posted on 2023-06-08, 19:50 authored by C Meier, Erika ManciniErika Mancini, D H Bamford, M A Walsh, D I Stuart, J M Grimes
The problems encountered during the phasing and structure determination of the packaging enzyme P4 from bacteriophage f13 using the anomalous signal from selenium in a single-wavelength anomalous dispersion experiment (SAD) are described. The oligomeric state of P4 in the virus is a hexamer (with sixfold rotational symmetry) and it crystallizes in space group C2, with four hexamers in the crystallographic asymmetric unit. Current state-of-the-art ab initio phasing software yielded solutions consisting of 96 atoms arranged as sixfold symmetric clusters of Se atoms. However, although these solutions showed high correlation coefficients indicative that the substructure had been solved, the resulting phases produced uninterpretable electron-density maps. Only after further analysis were correct solutions found (also of 96 atoms), leading to the eventual identification of the positions of 120 Se atoms. Here, it is demonstrated how the difficulties in finding a correct phase solution arise from an intricate false-minima problem. © 2005 International Union of Crystallography - all rights reserved.

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Publication status

  • Published

File Version

  • Published version

Journal

Acta Crystallographica Section D: Biological Crystallography

ISSN

0907-4449

Publisher

International Union of Crystallography

Issue

9

Volume

61

Page range

1238-1244

Department affiliated with

  • Biochemistry Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2015-01-29

First Open Access (FOA) Date

2015-01-29

First Compliant Deposit (FCD) Date

2015-01-29

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