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

Date Published: September 01, 2017

Publisher: International Union of Crystallography

Author(s): Jill Trewhella, Anthony P. Duff, Dominique Durand, Frank Gabel, J. Mitchell Guss, Wayne A. Hendrickson, Greg L. Hura, David A. Jacques, Nigel M. Kirby, Ann H. Kwan, Javier Pérez, Lois Pollack, Timothy M. Ryan, Andrej Sali, Dina Schneidman-Duhovny, Torsten Schwede, Dmitri I. Svergun, Masaaki Sugiyama, John A. Tainer, Patrice Vachette, John Westbrook, Andrew E. Whitten.

http://doi.org/10.1107/S2059798317011597

Abstract

Updated guidelines are presented for publishing biomolecular small-angle scattering (SAS) experiments so that readers can independently assess the quality of the data and models presented. The focus is on solution scattering experiments with either X-rays (SAXS) or neutrons (SANS), where the primary goal is the generation and testing of three-dimensional models, particularly in the context of integrative/hybrid structural modelling.

Partial Text

The objective of publishing the preliminary guidelines for biomolecular small-angle scattering (SAS) experiments (Jacques, Guss, Svergun et al., 2012 ▸; Jacques, Guss & Trewhella, 2012 ▸) was to provide a reporting framework so that ‘readers can independently assess the quality of the data and the basis for any interpretations presented’. The focus was on solution SAS experiments, both small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), where the primary goal is the generation and testing of three-dimensional models. The 2012 guidelines, which were developed in consultation with members of the SAS and Journals Commissions of the IUCr and other experts in the field, are now used by many authors and are endorsed by IUCr Journals (http://journals.iucr.org/services/sas/).

The following section, together with Figs. 1–4, Supplementary Fig. S1 and Tables 5 ▸(a)–5 ▸(g), describes the conduct and results of a set of SEC–SAXS experiments on solutions of glucose isomerase (GI; a well characterized tetramer in solution; Ramagopal et al., 2003 ▸), bovine serum albumin (BSA; a two-domain protein with a flexible loop connecting its domains and known to be prone to oligomerization) and Ca2+-bound calmodulin (CaM; a two-domain protein known to have an extended helix with a highly mobile region linking two domains that in solution move independently; Babu et al., 1988 ▸; Barbato et al., 1992 ▸; Heidorn & Trewhella, 1988 ▸). The example data sets were deliberately selected to be well characterized protein structures, but not necessarily ideal measurements, in order to demonstrate how the reporting guidelines aid in both data assessment and model evaluation and in assembling a comprehensive description of the experiment and the models that the data support. The tabulated results for all three proteins provided the subset of information required for the deposition of metadata, data and models in the SASBDB (deposition IDs are provided in Table 5 ▸g).

The example SEC–SAXS experiments on GI, BSA and CaM illustrate the value of comprehensive reporting so that data quality and model accuracy are clearly communicated. Supplementary Table S1 provides a guide for tabulating the recommended information for a general SAXS experiment; such a table will be included in future releases of the IUCr Journals Word template. Some publishers may well require much of the reporting to be included as supplementary material. Eventually, most of it should be made available via the developing SAXS data and model archives. The latter will be increasingly important for managing related data sets, although Figs. 2, 3, 4 and 5 in Carter et al. (2015 ▸) show how effectively one can assemble the results for multiple data sets.

 

Source:

http://doi.org/10.1107/S2059798317011597

 

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