[phenixbb] Re: PDB deposition question: processed data in P6₃22, refined model in P6₃

Dear Betul, Please process the diffraction data in P63 is you mean to refine the structure in that space group. ============================================= CHENGHUA SHAO, Ph.D. Scientific Software Developer, RCSB Protein Data Bank Assistant Research Professor, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4968 | E: [email protected] rcsb.org | iqb.rutgers.edu | facebook https://www.facebook.com/RCSBPDB | twitter https://twitter.com/buildmodels | PDB-Carbohydrate https://doi.org/10.1093/glycob/cwab039 On 7/1/26 16:17, Tom Peat via phenixbb wrote:

Hello Betul,

The data and structure should have the same space group. I'm not sure if the PDB would allow deposition if the two didn't match. I would spend a little time to figure out which space group your data are in- clearly there seems to be some ambiguity and then re-refine the model in the appropriate space group. Best of luck, Tom ________________________________ From:[email protected] Sent: Thursday, July 2, 2026 2:29 AM To:[email protected] Subject: [phenixbb] PDB deposition question: processed data in P6₃22, refined model in P6₃

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Hello everyone,



I have a question regarding PDB deposition.



The processed diffraction data are in P6₃22, while the refined structure is in P6₃. During PDB deposition, the validation server reports a completeness of only ~51% which appears to result from the difference in symmetry between the processed data and the refined model.



Would it be acceptable to deposit the structure in this situation, or should the diffraction data be reprocessed in P6₃ and refined again before deposition?



Thank you very much for your advice!

Best, Betul _______________________________________________ phenixbb mailing list [email protected] To unsubscribe send an email [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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