[3dem] Improved OneDep Support for 3D ED/MicroED

[Justin Flatt]

With the recent advancement of 3D Microcrystal Electron Diffraction (3D 
ED/MicroED), the number of Electron Crystallography structures deposited 
in the Protein Data Bank (PDB) has increased and expect to continue 
growing rapidly. This growth has highlighted the community need to 
improve PDB data deposition and representation to support this 
technology.

Since 2023, wwPDB has been working with 3D ED/MicroED community experts 
and mmCIF Working Group to develop a new data model [1] as an extension 
of the PDBx/mmCIF dictionary. Following community recommendations, the 
metadata of 3D ED/MicroED structures are now collected using the 
Macromolecular Crystallography framework, with additional metadata for 
data collection and processing protocols pertains to this unique 
technology.

This new model of 3D ED/MicroED has been incorporated into wwPDB OneDep 
deposition system to collect improved metadata, including microcrystal 
preparation, continuous rotation data collection, and controlled 
electron fluence. Structure factors are now required for submission 
(rather than derived map files). These structure factors are then used 
to generate the corresponding validation reports.

Support has also been added for SerialED metadata collection through the 
PDBx/mmCIF Serial Crystallography [2] extension.

In the near future, existing Electron Crystallography entries in the PDB 
will be remediated to conform to this data model.

_Example data collected for X-ray, 3D ED/MicroED, and 3DEM structure 
solution procedures_

Links:
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[1] https://urldefense.com/v3/__https://github.com/wwPDB/microed-extension__;!!Mih3wA!FYL1wzuZFeZtw_KSioRl63HN7dFub5OYEUwHkA5_g1jO3ok4pC6CmbJSd6LM8y2wPnB3rM-0XaJ66rNRAvWEl1hJ$ 
[2] https://urldefense.com/v3/__https://github.com/pdbxmmcifwg/xfel-extension__;!!Mih3wA!FYL1wzuZFeZtw_KSioRl63HN7dFub5OYEUwHkA5_g1jO3ok4pC6CmbJSd6LM8y2wPnB3rM-0XaJ66rNRAqJsg1cR$ 
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