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

Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

doi:10.1107/S2059798318005764

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:

; Adams, Paul D.; Urzhumtsev, Alexandre

Publication Date:: Fri Jun 08 00:00:00 EDT 2018

Research Org.:: Lawrence Berkeley National Laboratory (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.

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                    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.  https://doi.org/10.1107/S2059798318005764

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                    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.  https://doi.org/10.1107/S2059798318005764.

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@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         = {Fri Jun 08 00:00:00 EDT 2018},

  month        = {Fri Jun 08 00:00:00 EDT 2018}

}

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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 »

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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

Citation Formats

Figures / Tables:

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

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

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

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

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

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

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

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

Domain flexibility in aspartic proteinases journal, February 1992

Comparing anisotropic displacement parameters in protein structures journal, December 1999

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

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

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

TLS from fundamentals to practice journal, October 2013

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

The Structure and Thermal Motion of the B800–850 LH2 Complex from Rps.acidophila at 2.0Å Resolution and 100K: New Structural Features and Functionally Relevant Motions journal, March 2003

PHENIX: a comprehensive Python-based system for macromolecular structure solution journal, January 2010

On Information and Sufficiency journal, March 1951

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

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

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

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

The Protein Data Bank journal, January 2000

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

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

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

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Insights into the Binding of Pyridines to the Iron–Sulfur Enzyme IspH
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Validation of crystallographic models containing TLS or other descriptions of anisotropy
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Exploring the Structural Dynamics of the E.coli Chaperonin GroEL Using Translation-libration-screw Crystallographic Refinement of Intermediate States
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Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage1 1Edited by K. Morikawa
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Refinement of the arginine kinase transition-state analogue complex at 1.2 Å resolution: mechanistic insights
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Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

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

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

Domain flexibility in aspartic proteinases
journal, February 1992

Comparing anisotropic displacement parameters in protein structures
journal, December 1999

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

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

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

TLS from fundamentals to practice
journal, October 2013

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

The Structure and Thermal Motion of the B800–850 LH2 Complex from Rps.acidophila at 2.0Å Resolution and 100K: New Structural Features and Functionally Relevant Motions
journal, March 2003

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

On Information and Sufficiency
journal, March 1951

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

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

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

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journal, March 2006

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

The Protein Data Bank
journal, January 2000

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

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

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

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

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

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