While I agree with testing in lower symmetry (and I'm sure you have), it is also possible that the asymmetry is too slight or doesn't affect the crystals contacts, so that the dimer would orient randomly as it packs into the crystal. In that case, taking the average over all asymmetric units, the crystal really does have the higher symmetry and you would have to use alternate conformations as you are doing. I believe a case of this is Mario Amzel's F1 ATPase (pdb 1MAB) which crystallized in 1H32. The ATPase (ATP synthase we would call it today) catalytic subunits are known to form an asymmetric trimer but it apparently crystallized with that trimer axis on the 3-fold crystallographic axis. The data clearly justified The higher symmetry (according to the authors). Later structures with the entire assembly in the asymmetric unit give us a good picture of the three different protomers, and it would be interesting to go back and try to model it with 3 alternate conformations in each asym m etric unit of Amzel's structure.
On 04/03/2019 04:36 AM, Daniele de Sanctis wrote:
Hi all, we have a structure with a pseudo internal symmetry along a 2-fold axis that sits on a 2-fold crystallographic axis. For refinement purposes we have modeled the parts that differ with 50% occupancy, but before depositing the structure we wanted to make sure that this is the best way to deal with it and it is in agreement with PDB standards. Did anyone deal with similar cases in the past? Cheers Daniele -- ἀρετή --------------------------------------- Daniele de Sanctis Structural Biology Group ESRF - The European Synchrotron Grenoble, France Tel 33 (0)4 76 88 2869 http://www.esrf.eu/id29 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.esrf.eu_id29&d=DwMFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=vnEj1abxMFUnzn17cJg_YOzClbaPz8g9uMYkvdi3Vpk&s=wioldKL29BF5TO-puyT5A0VZ9imL2EwIP30IMViFouU&e=> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=vnEj1abxMFUnzn17cJg_YOzClbaPz8g9uMYkvdi3Vpk&s=SChbPEp5LO1WFokOxCV2mqRZbydshTtsOlkXsMYgH3M&e=>
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