Improved OneDep Support for 3D ED/MicroED

IP
Irina Persikova
Thu, Jul 30, 2026 2:26 PM

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
https://github.com/wwPDB/microed-extension 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
https://github.com/pdbxmmcifwg/xfel-extension extension.

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

Read the full news here:
https://www.wwpdb.org/news/news?year=2026#6a3ab4590fba48755e860645

On behalf of the wwPDB,

--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@rcsb.org
mailto:irina.persikova@rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu http://iqb.rutgers.edu |
facebook https://www.facebook.com/RCSBPDB | twitter
https://twitter.com/buildmodels

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 <https://github.com/wwPDB/microed-extension> 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 <https://github.com/pdbxmmcifwg/xfel-extension> extension. In the near future, existing Electron Crystallography entries in the PDB will be remediated to conform to this data model. Read the full news here: https://www.wwpdb.org/news/news?year=2026#6a3ab4590fba48755e860645 On behalf of the wwPDB, -- IRINA PERSIKOVA, Ph.D. Deputy Biocuration Lead, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4938 | E: irina.persikova@rcsb.org <mailto:irina.persikova@rcsb.org> rcsb.org <www.rcsb.org> | iqb.rutgers.edu <http://iqb.rutgers.edu> | facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels>