2017-01-18 : 4464 EMDB map entries, 1427 PDB coordinate entries PDBe | RCSB    

One-stop shop for 3DEM deposition and retrieval



3DEM Validation Pipeline

EMDataBank is working with the wwPDB to develop validation reports for deposited 3DEM structures. Currently, 3DEM validation reports provide information on model stereochemistry using the same criteria as provided for X-ray and NMR structures.

As of January 2016, validation reports for 3DEM structures are available to depositors at the time of deposition via the wwPDB Deposition and Annotation System.

As of May 2016, validation reports are also available for 3DEM entries in the PDB archive that have been publically released (news item).

Validation Services

Fourier Shell Correlation (FSC) Server: Upload two independent maps, receive the calculated FSC curve in a standardized format for deposition into EMDB, view and download a plot of the FSC curve (example plot). Developed and hosted at PDBe.

Tilt-Pair Server: Validate map hand and overall shape for lower resolution maps in which secondary structure features are absent. This server, originally developed by the Rosenthal group (Wasilewski et al J. Struct Biol 2014), has been migrated to PDBe.

3DEM Validation Task Force

The Electron Microscopy Validation Task Force (EM VTF) met on September 28-29, 2010 at Rutgers University in New Brunswick NJ. Twenty highly regarded EM scientists from around the world assembled to consider possible validation standards for 3D maps and models produced by electron microscopy reconstruction methods. The workshop was co-chaired by Richard Henderson (MRC, Cambridge) for map validation and Andrej Sali (UCSF) for model validation. The EM VTF's initial recommendations are published here: Henderson et al (2012), Structure 20, 205-214.