Raw experimental data for 3D structures highlighted at PDBe

PDBe raw experimental data component
02 August 2018

PDBe, IRRMC, SBGrid, EMPIAR and BMRB are pleased to announce a web component available on the PDBe web pages that enables users to easily access unprocessed experimental data associated with PDB structures.

When viewing and interpreting structures in the PDB, the model you are looking at is an interpretation of the underlying experimental data. To ensure models can be validated, deposition of a processed representation of these data is mandatory alongside the PDB model. For X-ray diffraction entries the structure factors must be provided, for Electron Microscopy the electric potential map must be deposited to EMDB, and for Nuclear Magnetic Resonance (NMR) entries the chemical shifts and restraints must also be provided.

The component provides summary information and links to available unprocessed experimental data from the following resources:

Archive Experimental Data Available Example PDB entry
Biological Magnetic Resonance Bank (BMRB) Nuclear magnetic resonance (NMR) spectroscopic data pdbe.org/2kpn
SBGrid Databank X-ray diffraction image data pdbe.org/5tok
Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) X-ray diffraction image data pdbe.org/4weq
Electron Microscopy Public Image Archive (EMPIAR) Raw electron microscopy image datasets pdbe.org/3j7n


The unprocessed images in crystallography, electron microscopy and the free induction decay data in NMR can be costly to archive, and while not mandatory, they are currently encouraged by wwPDB for deposition in specialised archives. These data can of course be used for assessing reproducibility of the published results, but they can also be used for methods development. This new component is a convenient tool to access relevant unprocessed datasets in the context of viewing information about an individual PDB structure.