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Electron Diffraction Dictionary Update Documentation

Title: Electron Diffraction Dictionary Extension
Author: C. Shao, E. Peisach
Date: 21-Oct-2025
email: chenghua.shao@rcsb.org

This document provides an overview of extensions to support metadata collection and annotation of PDB structures resolved by Electron Diffraction methods, especially by 3D ED/MicroED method. Listed below are the NEW data items designed for Electron Diffraction methods.

pdbx_exptl_subtype

Data items in the PDBX_EXPTL_SUBTYPE category record details about the method subtype under the primary method recorded in _exptl.method

  • _pdbx_exptl_subtype.exptl_method : This data item is a pointer to _exptl.method in the EXPTL category.

  • _pdbx_exptl_subtype.method_type : The subtype of the method used in the experiment. The subtype should be a variance of the primary method recorded in the _exptl.method item, with distinctive technical applications and significant scientific impacts.

    Enumeration:

    * Microcrystal Electron Diffraction
* 2-Dimensional Electron Crystallography

  • _pdbx_exptl_subtype.details : Details about the method subtype.

pdbx_exptl_crystal_process

Data items in the pdbx_exptl_crystal_process category record details of the post-crystallization process to prepare specific crystal samples such as microcrystals for subsequent diffraction experiments.

  • _pdbx_exptl_crystal_process.id : The ordinal identifier for the category

  • _pdbx_exptl_crystal_process.crystal_id : This data item is a pointer to the _exptl_crystal.id

  • _pdbx_exptl_crystal_process.microcrystal_method : The method used to produce microcrystals for diffraction experiments, if applicable.

    Enumeration:

    * Vortexing
* Other
* FIB milling
* Naturally grown
* Sonication

  • _pdbx_exptl_crystal_process.microcrystal_instrument : The instrument used to produce microcrystals for the experiments, if applicable.

  • _pdbx_exptl_crystal_process.microcrystal_min_dim : The minimal dimension of the final crystal ready for diffraction experiments. For example, for microcrystals processed by FIB milling, this item refers to the thickness of the thin lamella.

  • _pdbx_exptl_crystal_process.microcrystal_max_dim : The maximal dimension of the final crystal ready for diffraction experiments. For example, for microcrystals processed by FIB milling, this item refers to the length of the thin lamella.

  • _pdbx_exptl_crystal_process.microcrystal_description : Characteristics of the final crystal ready for diffraction experiments, e.g. shape.

  • _pdbx_exptl_crystal_process.details : The details about the crystal process.

pdbx_exptl_crystal_cryo_treatment

Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal.

  • _pdbx_exptl_crystal_cryo_treatment.cryogen : The name of cryogen used for vitrification

    Enumeration:

    * ETHANE
* NITROGEN
* OTHER

diffrn_measurement

Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured.

  • _diffrn_measurement.pdbx_angle_start : The starting angle for crystal rotation.

  • _diffrn_measurement.pdbx_angle_end : The ending angle for crystal rotation.

  • _diffrn_measurement.pdbx_rotation_rate : The speed of crystal rotation.

  • _diffrn_measurement.pdbx_exposure_time_per_image : The exposure time per image for the crystal and detector/camera.

  • _diffrn_measurement.rotation_mode : Originated from IUCr Electron Diffraction CIF extension. Code describing the technique used to sample as completely as possible the accessible range of reciprocal space. Rotation mode indicates the detector records diffracted intensities continuously while the sample is rotated. Stepwise model indicates the detector records diffracted intensities while the sample is stationary.

    Enumeration:

    * rotation
* stepwise

  • _diffrn_measurement.method_precession : Originated from IUCr Electron Diffraction CIF extension. Flag indicating if the radiation beam illuminates the sample at an angle that is rotated about a precession axis.

    Enumeration:

    * N
* Y

  • _diffrn_measurement.sample_tracking : Originated from IUCr Electron Diffraction CIF extension. Flag indicating if a tracking method to follow the crystal was used in the data acquisition. Typically used to track very small crystals in electron diffraction experiments.

    Enumeration:

    * N
* Y

  • _diffrn_measurement.sample_tracking_method : Originated from IUCr Electron Diffraction CIF extension. Description of the method used to follow the crystal during data collection.

pdbx_diffrn_ed

Data items in the PDBX_DIFFRN_ED record details specific to electron diffraction method.

  • _pdbx_diffrn_ed.id : This ordinal identifier for the category

  • _pdbx_diffrn_ed.diffrn_id : This data item is a pointer to the _diffrn.id

  • _pdbx_diffrn_ed.electron_source : The source of electrons, i.e. the electron gun

    Enumeration:

    * OTHER
* FIELD EMISSION GUN
* LAB6

  • _pdbx_diffrn_ed.beam_diameter_sample_plane : The electron beam diameter at the sample plane

  • _pdbx_diffrn_ed.camera_length : The product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode.

  • _pdbx_diffrn_ed.recording_mode : The mode of the detector for electron diffraction recording, e.g. Electron Counting (Event) mode, Linear (Integrating) mode

    Enumeration:

    * Other
* Integrating
* Electron Counting

  • _pdbx_diffrn_ed.fluence_rate : Fluence rate, or flux density at the sample plane

  • _pdbx_diffrn_ed.fluence_accumulated : Total fluence at the sample plane

  • _pdbx_diffrn_ed.c2_aperture_diameter : C2 aperture diameter

  • _pdbx_diffrn_ed.sa_aperture_diameter : Select Area aperture diameter

  • _pdbx_diffrn_ed.energyfilter_name : The name of the energy filter

  • _pdbx_diffrn_ed.energyfilter_upper : The energy filter range upper value in electron volts (eV) set by the specrometer

  • _pdbx_diffrn_ed.energyfilter_lower : The energy filter range lower value in electron volts (eV) set by the specrometer

  • _pdbx_diffrn_ed.details : Details of the electron diffration process