Repository logo
 

Au courant computation of the PDB to audit diffraction anisotropy of soluble and membrane proteins.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Robert, Xavier 
Kassis-Sahyoun, Josiane 
Ceres, Nicoletta 
Martin, Juliette 
Sawaya, Michael R 

Abstract

This data article makes available the informed computation of the whole Protein Data Bank (PDB) to investigate diffraction anisotropy on a large scale and to perform statistics. This data has been investigated in detail in "X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins" [1]. Diffraction anisotropy is traditionally associated with absence of contacts in-between macromolecules within the crystals in a given direction of space. There are however many case that do not follow this empirical rule. To investigate and sort out this discrepancy, we computed diffraction anisotropy for every entry of the PDB, and put them in context of relevant metrics to compare X-ray diffraction in reciprocal space to the crystal packing in real space. These metrics were either extracted from PDB files when available (resolution, space groups, cell parameters, solvent content), or calculated using standard procedures (anisotropy, crystal contacts, presence of ligands). More specifically, we separated entries to compare soluble vs membrane proteins, and further separated the later in subcategories according to their insertion in the membrane, function, or type of crystallization (Type I vs Type II crystal packing). This informed database is being made available to investigators in the raw and curated formats that can be re-used for further downstream studies. This dataset is useful to test ideas and to ascertain hypothesis based on statistical analysis.

Description

Keywords

Diffraction anisotropy, Macromolecule crystals, Membrane proteins, X-ray diffraction

Journal Title

Data Brief

Conference Name

Journal ISSN

2352-3409
2352-3409

Volume Title

19

Publisher

Elsevier BV
Sponsorship
Wellcome Trust (209407/Z/17/Z)