CryoEM Data Archiving and Validation: Community Recommendations

What is it about?

A workshop was held at EMBL-EBI in January 2020 to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. The report describes the workshop's motivation, history, topics discussed, and consensus recommendations. Challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations. The results of structural studies by macromolecular crystallography, NMR, and 3DEM have been captured in the single global archive of atomic models of biomacromolecules and their complexes, the Protein Data Bank (PDB). With great foresight, the protein crystallography community established this archive in 1971, which has turned out to be a landmark event in the history of public archiving of open scientific data. The PDB was originally hosted at Brookhaven National Laboratory. Since the early 2000s, the PDB has been managed and operated through the Worldwide Protein Data Bank (wwPDB), a collaboration involving five partners across the USA, Europe and Japan. In addition to atomic models, the PDB also captures some derived experimental data, namely crystallographic structure factors and NMR chemical shifts and restraints. The Electron Microscopy Data Bank (EMDB) was established in 2002 to archive processed experimental data from a variety of 3DEM modalities, most notably single-particle analysis (SPA), electron tomography, subtomogram averaging (STA), helical reconstruction (HR) and electron crystallography (EC). These modalities all produce data from which 3D volumes can ultimately be determined.

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Why is it important?

The research is important because it discusses data requirements for the deposition and validation of cryoEM structures, which has a focus on single-particle analysis. The meeting was attended by experts in data processing, model building and refinement, validation, and archiving of such structures, which highlights the significance of the research. Key Takeaways: 1. The workshop aimed to discuss data requirements for the deposition and validation of cryoEM structures with a focus on single-particle analysis. 2. The Protein Data Bank (PDB) captures atomic models and derived experimental data from macromolecular crystallography, NMR and 3DEM. 3. The need for validation in 3DEM was emphasized due to the varying reliability of structural models produced, particularly when the resolution of the experimental data was low. 4. Validation techniques, metrics, and recommendations for good practice were developed to minimize the likelihood of serious errors going undetected and making it into final models.