Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs.

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment forab initioshape reconstruction from scattering data. The inherent variability of theab initioshapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions ofab initioSAS models.

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Low-Resolution Structure of Detergent-Solubilized Membrane Proteins from Small-Angle Scattering Data

Biophysical Journal ◽

10.1016/j.bpj.2017.10.003 ◽

2017 ◽

Vol 113 (11) ◽

pp. 2373-2382 ◽

Cited By ~ 10

Author(s):

Alexandros Koutsioubas

Keyword(s):

Membrane Proteins ◽

Small Angle ◽

Small Angle Scattering ◽

Scattering Data ◽

Low Resolution ◽

Angle Scattering ◽

Resolution Structure

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ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions

Journal of Applied Crystallography ◽

10.1107/s1600576717007786 ◽

2017 ◽

Vol 50 (4) ◽

pp. 1212-1225 ◽

Cited By ~ 620

Author(s):

D. Franke ◽

M. V. Petoukhov ◽

P. V. Konarev ◽

A. Panjkovich ◽

A. Tuukkanen ◽

...

Keyword(s):

Experimental Data ◽

High Resolution ◽

Ab Initio ◽

Small Angle ◽

Small Angle Scattering ◽

Size Exclusion ◽

Scattering Data ◽

Mode Analysis ◽

Angle Scattering ◽

High Resolution Models

ATSASis a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment,ab initiobead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8ATSASrelease series and highlights the latest developments. These includeAMBIMETER, an assessment of the reconstruction ambiguity of experimental data;DATCLASS, a multiclass shape classification based on experimental data;SASRES, for estimating the resolution ofab initiomodel reconstructions;CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data;SHANUM, to evaluate the useful angular range in measured data;SREFLEX, to refine available high-resolution models using normal mode analysis;SUPALMfor a rapid superposition of low- and high-resolution models; andSASPy, theATSASplugin for interactive modelling inPyMOL. All these features and other improvements are included in theATSASrelease 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.

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AB Initio Tertiary Structure Prediction from Small Angle Scattering Data

Biophysical Journal ◽

10.1016/j.bpj.2019.11.2666 ◽

2020 ◽

Vol 118 (3) ◽

pp. 481a

Author(s):

Christopher Prior ◽

Ehmke Pohl ◽

Owen Davies

Keyword(s):

Ab Initio ◽

Small Angle ◽

Structure Prediction ◽

Tertiary Structure ◽

Small Angle Scattering ◽

Scattering Data ◽

Tertiary Structure Prediction ◽

Angle Scattering

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2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317011597 ◽

2017 ◽

Vol 73 (9) ◽

pp. 710-728 ◽

Cited By ~ 107

Author(s):

Jill Trewhella ◽

Anthony P. Duff ◽

Dominique Durand ◽

Frank Gabel ◽

J. Mitchell Guss ◽

...

Keyword(s):

Small Angle ◽

Task Force ◽

Data Bank ◽

Small Angle Scattering ◽

Scattering Data ◽

Quality Data ◽

Angle Scattering ◽

Publication Guidelines ◽

Guidelines And Recommendations

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

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