Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

Zuo, Xiaobing; Tiede, David M.

doi:10.1107/S1600576724007222

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

Journal Article · Tue Sep 17 04:00:00 EDT 2024 · Journal of Applied Crystallography (Online)

DOI:https://doi.org/10.1107/S1600576724007222· OSTI ID:2446735

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X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: NONE; AC02-06CH11357

OSTI ID:: 2446735

Journal Information:: Journal of Applied Crystallography (Online), Journal Name: Journal of Applied Crystallography (Online) Journal Issue: 5 Vol. 57; ISSN JACGAR; ISSN 1600-5767

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: Denmark

Language:: English

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