On the correlation between the main-chain and side-chain atomic displacement parameters (B values) in high-resolution protein structures

S. Parthasarathy, M. R N Murthy

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Correlation coefficients (CCs) between the mean atomic displacement parameters (B values) of the main-chain and the side-chain atoms in selected high-resolution protein structures are distributed over a broad range (0.5-1.0). The distribution of CCs is found to be related to the mean difference in B values of C(α) and C(β) atoms. High CCs are also associated with the frequent occurrence of consecutive C(α) atoms with relatively high B values. The distribution of CCs and its relation to the mean difference between the B values of C(α) and C(β) atoms shows dependence on the package used for refinement (X-PLOR, PROLSQ or TNT). These observations reflect the differences in the way B-value constraints are handled in these packages. Further differences are discernible in the distributions for proteins refined using the same package. It is likely that these differences are related to the different refinement protocols or weighting schemes followed by investigators. The resolution of these issues is important for evolving correct strategies for the refinement of the atomic displacement parameters in X-ray diffraction studies of proteins. Furthermore, it may be possible to develop refinement-validation tools by observing the features that are invariant in the distribution of atomic displacement parameters.

Original languageEnglish (US)
Pages (from-to)173-180
Number of pages8
JournalActa Crystallographica Section D: Biological Crystallography
Volume55
Issue number1
StatePublished - Jan 1 1999
Externally publishedYes

Fingerprint

correlation coefficients
proteins
Atoms
high resolution
Trinitrotoluene
atoms
Proteins
X-Ray Diffraction
trinitrotoluene
Research Personnel
occurrences
X ray diffraction
diffraction
x rays

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Condensed Matter Physics
  • Structural Biology

Cite this

On the correlation between the main-chain and side-chain atomic displacement parameters (B values) in high-resolution protein structures. / Parthasarathy, S.; Murthy, M. R N.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 55, No. 1, 01.01.1999, p. 173-180.

Research output: Contribution to journalArticle

@article{db385b86d91f4a578276edda65f67e2f,
title = "On the correlation between the main-chain and side-chain atomic displacement parameters (B values) in high-resolution protein structures",
abstract = "Correlation coefficients (CCs) between the mean atomic displacement parameters (B values) of the main-chain and the side-chain atoms in selected high-resolution protein structures are distributed over a broad range (0.5-1.0). The distribution of CCs is found to be related to the mean difference in B values of C(α) and C(β) atoms. High CCs are also associated with the frequent occurrence of consecutive C(α) atoms with relatively high B values. The distribution of CCs and its relation to the mean difference between the B values of C(α) and C(β) atoms shows dependence on the package used for refinement (X-PLOR, PROLSQ or TNT). These observations reflect the differences in the way B-value constraints are handled in these packages. Further differences are discernible in the distributions for proteins refined using the same package. It is likely that these differences are related to the different refinement protocols or weighting schemes followed by investigators. The resolution of these issues is important for evolving correct strategies for the refinement of the atomic displacement parameters in X-ray diffraction studies of proteins. Furthermore, it may be possible to develop refinement-validation tools by observing the features that are invariant in the distribution of atomic displacement parameters.",
author = "S. Parthasarathy and Murthy, {M. R N}",
year = "1999",
month = "1",
day = "1",
language = "English (US)",
volume = "55",
pages = "173--180",
journal = "Acta Crystallographica Section D: Structural Biology",
issn = "0907-4449",
publisher = "John Wiley and Sons Inc.",
number = "1",

}

TY - JOUR

T1 - On the correlation between the main-chain and side-chain atomic displacement parameters (B values) in high-resolution protein structures

AU - Parthasarathy, S.

AU - Murthy, M. R N

PY - 1999/1/1

Y1 - 1999/1/1

N2 - Correlation coefficients (CCs) between the mean atomic displacement parameters (B values) of the main-chain and the side-chain atoms in selected high-resolution protein structures are distributed over a broad range (0.5-1.0). The distribution of CCs is found to be related to the mean difference in B values of C(α) and C(β) atoms. High CCs are also associated with the frequent occurrence of consecutive C(α) atoms with relatively high B values. The distribution of CCs and its relation to the mean difference between the B values of C(α) and C(β) atoms shows dependence on the package used for refinement (X-PLOR, PROLSQ or TNT). These observations reflect the differences in the way B-value constraints are handled in these packages. Further differences are discernible in the distributions for proteins refined using the same package. It is likely that these differences are related to the different refinement protocols or weighting schemes followed by investigators. The resolution of these issues is important for evolving correct strategies for the refinement of the atomic displacement parameters in X-ray diffraction studies of proteins. Furthermore, it may be possible to develop refinement-validation tools by observing the features that are invariant in the distribution of atomic displacement parameters.

AB - Correlation coefficients (CCs) between the mean atomic displacement parameters (B values) of the main-chain and the side-chain atoms in selected high-resolution protein structures are distributed over a broad range (0.5-1.0). The distribution of CCs is found to be related to the mean difference in B values of C(α) and C(β) atoms. High CCs are also associated with the frequent occurrence of consecutive C(α) atoms with relatively high B values. The distribution of CCs and its relation to the mean difference between the B values of C(α) and C(β) atoms shows dependence on the package used for refinement (X-PLOR, PROLSQ or TNT). These observations reflect the differences in the way B-value constraints are handled in these packages. Further differences are discernible in the distributions for proteins refined using the same package. It is likely that these differences are related to the different refinement protocols or weighting schemes followed by investigators. The resolution of these issues is important for evolving correct strategies for the refinement of the atomic displacement parameters in X-ray diffraction studies of proteins. Furthermore, it may be possible to develop refinement-validation tools by observing the features that are invariant in the distribution of atomic displacement parameters.

UR - http://www.scopus.com/inward/record.url?scp=0032922192&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032922192&partnerID=8YFLogxK

M3 - Article

VL - 55

SP - 173

EP - 180

JO - Acta Crystallographica Section D: Structural Biology

JF - Acta Crystallographica Section D: Structural Biology

SN - 0907-4449

IS - 1

ER -