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Title: From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

Abstract

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63–76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both procedures are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.

Authors:
ORCiD logo; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1441078
Alternate Identifier(s):
OSTI ID: 1506324
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Volume: 74 Journal Issue: 7; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; TLS model; TLS refinement; atomic displacement parameters; rigid-body motion; ensemble of atomic models; atomic model validation; PDB

Citation Formats

Afonine, Pavel V., Adams, Paul D., and Urzhumtsev, Alexandre. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. United Kingdom: N. p., 2018. Web. doi:10.1107/S2059798318005764.
Afonine, Pavel V., Adams, Paul D., & Urzhumtsev, Alexandre. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. United Kingdom. doi:10.1107/S2059798318005764.
Afonine, Pavel V., Adams, Paul D., and Urzhumtsev, Alexandre. Fri . "From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation". United Kingdom. doi:10.1107/S2059798318005764.
@article{osti_1441078,
title = {From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation},
author = {Afonine, Pavel V. and Adams, Paul D. and Urzhumtsev, Alexandre},
abstractNote = {TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63–76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both procedures are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.},
doi = {10.1107/S2059798318005764},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 7,
volume = 74,
place = {United Kingdom},
year = {2018},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1107/S2059798318005764

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Cited by: 2 works
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Figures / Tables:

Figure 1 Figure 1: (a) A schematic representation of the atomic displacement for pure vibrations along the vertical axis (light and dark blue arrows) and (b) for libration around the axis perpendicular to the view (light and dark red arrows) shown for a five-atom dummy model (black dots). Lighter coloured arrows correspondmore » to displacements with larger amplitudes. The displacements for vibration and libration are similar for small amplitudes and different for large amplitudes (b). The curvature of libration displacements with large amplitudes (b) makes them anharmonic.« less

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Works referenced in this record:

Insights into the Binding of Pyridines to the Iron–Sulfur Enzyme IspH
journal, May 2014

  • Span, Ingrid; Wang, Ke; Eisenreich, Wolfgang
  • Journal of the American Chemical Society, Vol. 136, Issue 22
  • DOI: 10.1021/ja501127j

Validation of crystallographic models containing TLS or other descriptions of anisotropy
journal, July 2010

  • Zucker, Frank; Champ, P. Christoph; Merritt, Ethan A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 8
  • DOI: 10.1107/S0907444910020421

Exploring the Structural Dynamics of the E.coli Chaperonin GroEL Using Translation-libration-screw Crystallographic Refinement of Intermediate States
journal, September 2004

  • Chaudhry, Charu; Horwich, Arthur L.; Brunger, Axel T.
  • Journal of Molecular Biology, Vol. 342, Issue 1
  • DOI: 10.1016/j.jmb.2004.07.015

Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage1 1Edited by K. Morikawa
journal, April 2001

  • Raaijmakers, Hans; Törö, Imre; Birkenbihl, Rainer
  • Journal of Molecular Biology, Vol. 308, Issue 2
  • DOI: 10.1006/jmbi.2001.4592

Refinement of the arginine kinase transition-state analogue complex at 1.2 Å resolution: mechanistic insights
journal, November 2002

  • Yousef, Mohammad S.; Fabiola, Felcy; Gattis, James L.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 12
  • DOI: 10.1107/S0907444902014683

Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

From deep TLS validation to ensembles of atomic models built from elemental motions
journal, July 2015

  • Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 8
  • DOI: 10.1107/S1399004715011426

TLSANL : TLS parameter-analysis program for segmented anisotropic refinement of macromolecular structures
journal, August 1993


Some B eq are more equivalent than others
journal, October 2011

  • Merritt, Ethan A.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 67, Issue 6
  • DOI: 10.1107/S0108767311034350

Domain flexibility in aspartic proteinases
journal, February 1992

  • Šali, Andrej; Veerapandian, B.; Cooper, Jon B.
  • Proteins: Structure, Function, and Genetics, Vol. 12, Issue 2
  • DOI: 10.1002/prot.340120209

Comparing anisotropic displacement parameters in protein structures
journal, December 1999

  • Merritt, Ethan A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 12
  • DOI: 10.1107/S0907444999011853

Use of TLS parameters to model anisotropic displacements in macromolecular refinement
journal, January 2001

  • Winn, M. D.; Isupov, M. N.; Murshudov, G. N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 1
  • DOI: 10.1107/S0907444900014736

To B or not to B : a question of resolution?
journal, March 2012

  • Merritt, Ethan A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444911028320

A New Generation of Crystallographic Validation Tools for the Protein Data Bank
journal, October 2011


REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

TLS from fundamentals to practice
journal, October 2013


Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

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
  • DOI: 10.1107/S0907444909052925

On Information and Sufficiency
journal, March 1951

  • Kullback, S.; Leibler, R. A.
  • The Annals of Mathematical Statistics, Vol. 22, Issue 1
  • DOI: 10.1214/aoms/1177729694

Validation of Structures in the Protein Data Bank
journal, December 2017


Analysis of molecular motion with allowance for intramolecular torsion
journal, November 1978


Internal molecular motions in crystals. The estimation of force constants, frequencies and barriers from diffraction data. A feasibility study
journal, February 1983

  • Trueblood, K. N.; Dunitz, J. D.
  • Acta Crystallographica Section B Structural Science, Vol. 39, Issue 1
  • DOI: 10.1107/S0108768183002104

Errors in bond lengths due to rotational oscillations of molecules
journal, September 1956


The segmented anisotropic refinement of monoclinic papain by the application of the rigid-body TLS model and comparison to bovine ribonuclease A
journal, February 1992

  • Harris, G. W.; Pickersgill, R. W.; Howlin, B.
  • Acta Crystallographica Section B Structural Science, Vol. 48, Issue 1
  • DOI: 10.1107/S0108768191006663

Can X-ray data distinguish bonding effects from vibrational smearing?
journal, March 1976


Rigid protein motion as a model for crystallographic temperature factors.
journal, April 1991

  • Kuriyan, J.; Weis, W. I.
  • Proceedings of the National Academy of Sciences, Vol. 88, Issue 7
  • DOI: 10.1073/pnas.88.7.2773

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
journal, March 2006

  • Painter, Jay; Merritt, Ethan A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4
  • DOI: 10.1107/S0907444906005270

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum
journal, August 2016

  • Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9
  • DOI: 10.1107/S2059798316013048

The Protein Data Bank
journal, January 2000


Efficient anisotropic refinement of macromolecular structures using FFT
journal, January 1999

  • Murshudov, Garib N.; Vagin, Alexei A.; Lebedev, Andrey
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 1
  • DOI: 10.1107/S090744499801405X

On the rigid-body motion of molecules in crystals
journal, January 1968

  • Schomaker, V.; Trueblood, K. N.
  • Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 24, Issue 1
  • DOI: 10.1107/S0567740868001718

The protein data bank: A computer-based archival file for macromolecular structures
journal, May 1977

  • Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B.
  • Journal of Molecular Biology, Vol. 112, Issue 3
  • DOI: 10.1016/S0022-2836(77)80200-3

The 1.0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity
journal, September 2000

  • Wilson, Mark A.; Brunger, Axel T.
  • Journal of Molecular Biology, Vol. 301, Issue 5
  • DOI: 10.1006/jmbi.2000.4029

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles
journal, July 2015

  • Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 8
  • DOI: 10.1107/S1399004715007415

Non-rigid-body thermal-motion analysis
journal, January 1973