Small Angle Scattering and ab initio Modeling

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

BBA Advances ◽

10.1016/j.bbadva.2021.100033 ◽

2021 ◽

pp. 100033

Author(s):

Kerrie A. Morrison ◽

Aswin Doekhie ◽

George M. Neville ◽

Gareth J. Price ◽

Paul Whitley ◽

...

Keyword(s):

Membrane Proteins ◽

Ab Initio ◽

Small Angle ◽

Small Angle Scattering ◽

Scattering Data ◽

Angle Scattering

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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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