The accurate assessment of small-angle X-ray scattering data

Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.

doi:10.1107/S1399004714010876

Title: The accurate assessment of small-angle X-ray scattering data

Abstract

Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.

Authors:

Grant, Thomas D. ^[1]; Luft, Joseph R. ^[2]; Carter, Lester G. ^[3]; Matsui, Tsutomu ^[3]; Weiss, Thomas M. ^[3]; Martel, Anne ^[3]; Snell, Edward H. ^[2]

Hauptman-Woodward Medical Research Inst. (HWI), Buffalo, NY (United States)
Hauptman-Woodward Medical Research Inst. (HWI), Buffalo, NY (United States); SUNY Buffalo, Buffalo, NY (United States)
SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL).

Publication Date:: Fri Jan 23 00:00:00 EST 2015

Research Org.:: SLAC National Accelerator Lab., Menlo Park, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1221791

Grant/Contract Number:: AC03-76SF00515

Resource Type:: Accepted Manuscript

Journal Name:: Acta Crystallographica. Section D: Biological Crystallography (Online)

Additional Journal Information:: Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 71; Journal Issue: 1; Journal ID: ISSN 1399-0047

Publisher:: International Union of Crystallography

Country of Publication:: United States

Language:: English

Subject:: 36 MATERIALS SCIENCE; SAXS data quality; SAXStats

Citation Formats


                    Grant, Thomas D., Luft, Joseph R., Carter, Lester G., Matsui, Tsutomu, Weiss, Thomas M., Martel, Anne, and Snell, Edward H. The accurate assessment of small-angle X-ray scattering data.  United States: N. p., 2015. 
Web.  doi:10.1107/S1399004714010876.

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                    Grant, Thomas D., Luft, Joseph R., Carter, Lester G., Matsui, Tsutomu, Weiss, Thomas M., Martel, Anne, & Snell, Edward H. The accurate assessment of small-angle X-ray scattering data.  United States.  https://doi.org/10.1107/S1399004714010876

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                    Grant, Thomas D., Luft, Joseph R., Carter, Lester G., Matsui, Tsutomu, Weiss, Thomas M., Martel, Anne, and Snell, Edward H. Fri .  
"The accurate assessment of small-angle X-ray scattering data".  United States.  https://doi.org/10.1107/S1399004714010876.  https://www.osti.gov/servlets/purl/1221791.

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@article{osti_1221791,

  title        = {The accurate assessment of small-angle X-ray scattering data},

  author       = {Grant, Thomas D. and Luft, Joseph R. and Carter, Lester G. and Matsui, Tsutomu and Weiss, Thomas M. and Martel, Anne and Snell, Edward H.},

  abstractNote = {Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.},

  doi          = {10.1107/S1399004714010876},

  journal      = {Acta Crystallographica. Section D: Biological Crystallography (Online)},

  number       = 1,

  volume       = 71,

  place        = {United States},

  year         = {Fri Jan 23 00:00:00 EST 2015},

  month        = {Fri Jan 23 00:00:00 EST 2015}

}

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Works referencing / citing this record:

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Title: The accurate assessment of small-angle X-ray scattering data

Abstract

Citation Formats

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics journal, July 2001

Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg journal, May 2012

PEP: Predictions for Entire Proteomes journal, January 2003

TargetDB: a target registration database for structural genomics projects journal, May 2004

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source journal, January 2013

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Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution journal, May 2012

Small-angle scattering for structural biology-Expanding the frontier while avoiding the pitfalls journal, January 2010

Effects of ionizing radiations on proteins. Evidence of non-random fragmentations and a caution in the use of the method for determination of molecular mass journal, April 1990

Automatic target selection for structural genomics on eukaryotes journal, March 2004

CHOP proteins into structural domain-like fragments journal, April 2004

A deliberate approach to screening for initial crystallization conditions of biological macromolecules journal, April 2003

An integrated high-throughput data acquisition system for biological solution X-ray scattering studies journal, March 2012

Protein instability following transport or storage on dry ice journal, March 2013

Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering journal, February 2007

SAXS experiments on absolute scale with Kratky systems using water as a secondary standard journal, April 2000

Developing advanced X-ray scattering methods combined with crystallography and computation journal, March 2013

New developments in the ATSAS program package for small-angle scattering data analysis journal, March 2012

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution journal, August 2007

Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law journal, April 2011

GNOM – a program package for small-angle scattering data processing journal, October 1991

Biological small-angle X-ray scattering facility at the Stanford Synchrotron Radiation Laboratory journal, April 2007

Reduction of parasitic scattering in small-angle X-ray scattering by a three-pinhole collimating system journal, August 1990

The protein target list of the Northeast Structural Genomics Consortium journal, May 2004

The HDOCK server for integrated protein–protein docking journal, April 2020

Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation journal, February 2019

Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae journal, April 2018

Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles journal, June 2017

Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering data journal, August 2016

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics
journal, July 2001

Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg
journal, May 2012

PEP: Predictions for Entire Proteomes
journal, January 2003

TargetDB: a target registration database for structural genomics projects
journal, May 2004

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source
journal, January 2013

Automated acquisition and analysis of small angle X-ray scattering data
journal, October 2012

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journal, October 1977

SPINE 2: a system for collaborative structural proteomics within a federated database framework
journal, June 2003

Small angle X-ray scattering as a complementary tool for high-throughput structural studies
journal, April 2011

Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution
journal, May 2012

Small-angle scattering for structural biology-Expanding the frontier while avoiding the pitfalls
journal, January 2010

Effects of ionizing radiations on proteins. Evidence of non-random fragmentations and a caution in the use of the method for determination of molecular mass
journal, April 1990

Automatic target selection for structural genomics on eukaryotes
journal, March 2004

CHOP proteins into structural domain-like fragments
journal, April 2004

A deliberate approach to screening for initial crystallization conditions of biological macromolecules
journal, April 2003

An integrated high-throughput data acquisition system for biological solution X-ray scattering studies
journal, March 2012

Protein instability following transport or storage on dry ice
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Developing advanced X-ray scattering methods combined with crystallography and computation
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