Simulation of modulated protein crystal structure and diffraction data in a supercell and in superspace

Jeffrey J. Lovelace, Peter D. Simone, Václav Petříček, Gloria E Borgstahl

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The toolbox for computational protein crystallography is full of easy-to-use applications for the routine solution and refinement of periodic diffraction data sets and protein structures. There is a gap in the available software when it comes to aperiodic crystallographic data. Current protein crystallography software cannot handle modulated data, and small-molecule software for aperiodic crystallography cannot work with protein structures. To adapt software for modulated protein data requires training data to test and debug the changed software. Thus, a comprehensive training data set consisting of atomic positions with associated modulation functions and the modulated structure factors packaged as both a three-dimensional supercell and as a modulated structure in (3+1)D superspace has been created. The (3+1)D data were imported into Jana2006; this is the first time that this has been performed for protein data.

Original languageEnglish (US)
Pages (from-to)1062-1072
Number of pages11
JournalActa Crystallographica Section D: Biological Crystallography
Volume69
Issue number6
DOIs
StatePublished - Jun 1 2013

Fingerprint

Software
Crystallography
Proteins
Datasets

Keywords

  • average structure
  • disorder
  • modulated structures
  • protein
  • q vectors
  • satellite reflections
  • supercells
  • superspace

ASJC Scopus subject areas

  • Structural Biology

Cite this

Simulation of modulated protein crystal structure and diffraction data in a supercell and in superspace. / Lovelace, Jeffrey J.; Simone, Peter D.; Petříček, Václav; Borgstahl, Gloria E.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 69, No. 6, 01.06.2013, p. 1062-1072.

Research output: Contribution to journalArticle

@article{2dc2224646b147358126e866cdb4ed12,
title = "Simulation of modulated protein crystal structure and diffraction data in a supercell and in superspace",
abstract = "The toolbox for computational protein crystallography is full of easy-to-use applications for the routine solution and refinement of periodic diffraction data sets and protein structures. There is a gap in the available software when it comes to aperiodic crystallographic data. Current protein crystallography software cannot handle modulated data, and small-molecule software for aperiodic crystallography cannot work with protein structures. To adapt software for modulated protein data requires training data to test and debug the changed software. Thus, a comprehensive training data set consisting of atomic positions with associated modulation functions and the modulated structure factors packaged as both a three-dimensional supercell and as a modulated structure in (3+1)D superspace has been created. The (3+1)D data were imported into Jana2006; this is the first time that this has been performed for protein data.",
keywords = "average structure, disorder, modulated structures, protein, q vectors, satellite reflections, supercells, superspace",
author = "Lovelace, {Jeffrey J.} and Simone, {Peter D.} and V{\'a}clav Petř{\'i}ček and Borgstahl, {Gloria E}",
year = "2013",
month = "6",
day = "1",
doi = "10.1107/S0907444913004630",
language = "English (US)",
volume = "69",
pages = "1062--1072",
journal = "Acta Crystallographica Section D: Structural Biology",
issn = "0907-4449",
publisher = "John Wiley and Sons Inc.",
number = "6",

}

TY - JOUR

T1 - Simulation of modulated protein crystal structure and diffraction data in a supercell and in superspace

AU - Lovelace, Jeffrey J.

AU - Simone, Peter D.

AU - Petříček, Václav

AU - Borgstahl, Gloria E

PY - 2013/6/1

Y1 - 2013/6/1

N2 - The toolbox for computational protein crystallography is full of easy-to-use applications for the routine solution and refinement of periodic diffraction data sets and protein structures. There is a gap in the available software when it comes to aperiodic crystallographic data. Current protein crystallography software cannot handle modulated data, and small-molecule software for aperiodic crystallography cannot work with protein structures. To adapt software for modulated protein data requires training data to test and debug the changed software. Thus, a comprehensive training data set consisting of atomic positions with associated modulation functions and the modulated structure factors packaged as both a three-dimensional supercell and as a modulated structure in (3+1)D superspace has been created. The (3+1)D data were imported into Jana2006; this is the first time that this has been performed for protein data.

AB - The toolbox for computational protein crystallography is full of easy-to-use applications for the routine solution and refinement of periodic diffraction data sets and protein structures. There is a gap in the available software when it comes to aperiodic crystallographic data. Current protein crystallography software cannot handle modulated data, and small-molecule software for aperiodic crystallography cannot work with protein structures. To adapt software for modulated protein data requires training data to test and debug the changed software. Thus, a comprehensive training data set consisting of atomic positions with associated modulation functions and the modulated structure factors packaged as both a three-dimensional supercell and as a modulated structure in (3+1)D superspace has been created. The (3+1)D data were imported into Jana2006; this is the first time that this has been performed for protein data.

KW - average structure

KW - disorder

KW - modulated structures

KW - protein

KW - q vectors

KW - satellite reflections

KW - supercells

KW - superspace

UR - http://www.scopus.com/inward/record.url?scp=84878301328&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84878301328&partnerID=8YFLogxK

U2 - 10.1107/S0907444913004630

DO - 10.1107/S0907444913004630

M3 - Article

VL - 69

SP - 1062

EP - 1072

JO - Acta Crystallographica Section D: Structural Biology

JF - Acta Crystallographica Section D: Structural Biology

SN - 0907-4449

IS - 6

ER -