SASBDB, a repository for biological small-angle scattering data

Abstract

Small-angle X-ray and neutron scattering (SAXS and SANS) are fundamental tools used to study the global shapes of proteins, nucleic acids, macromolecular complexes and assemblies in solution. Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically. The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf). The small-angle scattering biological data bank (SASBDB) www.sasbdb.org has been designed in accordance with the plans of the SAStf as part of a future federated system of databases for biological SAXS and SANS. SASBDB is a comprehensive repository of freely accessible and fully searchable SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics. At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.

Figure 1.

Detailed representation of an SASBDB entry (based on http://www.sasbdb.org/data/SASDAU4/). (A) Title of the publication (or project in case of unpublished data). (B) List of authors, main contributor(s) to the SAS results highlighted in bold; journal reference and a link to PubMed if available. (C) SASBDB ID and the tile of the entry. (D) Name of the macromolecule(s) that were measured. (E) Experimental scattering data (logarithmic plot). (F, G) Fit to the experimental data from the respective model(s) displayed on the right. (H) Experimental details, buffer and a brief description of the data reduction steps. (I) Drop-down list of files available for download, including a zip archive with all files related to the entry. (J) Summary of the overall parameters: MW estimated from the forward scattering, molecular weight expected from the sequence and the oligomeric state, Porod volume. (K) Guinier plot with the linear fit and estimated values of the forward scattering I(0) and the radius of gyration R_g. (L) Dimensionless Kratky plot. (M) Distance distribution function p(r) and the maximum particle dimension D_max. (N) Ab initio model. (O) Hybrid model. On clicking the models switch to the interactive 3D mode. (P) Biological details of each measured macromolecule, sequence and a link to UniProt if available.

Figure 2.

Each SASBDB entry is organized around an experimental SAS data set that is linked to the metadata related to the experiment that includes the experimental conditions, derived structural parameters, real-space distance distribution, models and fits. Multiple entries can be grouped according to a publication or, in case of unpublished data, project. Links to external data banks such as PubMed, UniProt and PDB for the entry are provided.

Figure 3.

Brief representation of a SASBDB entry (browsing unit). (A) SASBDB ID and the title of the entry. (B) Experimental scattering data (logarithmic plot thumbnail). (C) One of the models. (D) Name of the macromolecule(s) that were measured, expected molecular weight organism, polymer type. Buffer details. Experiment type, instrument and data collection date. (E) Structural parameters: radius of gyration, maximum particle dimension, Porod volume. (F) Title of the publication (or project in case of unpublished data), journal reference, authors.