Hi,
When a homo-multimeric molecule has point group symmetry, it is very common for part of that symmetry to coincide with the space group symmetry. For instance, if a 222 (D2) tetramer crystallised in space group P222, a tetramer could sit at the intersection of 2 2-folds (1 monomer in the asymmetric unit), on a 2-fold (1 dimer or 2 monomers in the a.u.) or in a general position (4 monomers or one tetramer in the a.u.). In principle you could even have one of each, giving you a total of 7 monomers in the a.u., but all would be forming proper 222 tetramers in the crystal. So in your case the monomer model does match the crystallographic symmetry — you just have to make a dimer for visualisation by adding an appropriate symmetry copy.
Some time ago, Airlie McCoy added a feature to Phaser where, if the search model has point-group symmetry and it lands on a symmetry operator that agrees with that symmetry, it automatically removes the redundant copy that is generated by the space-group symmetry. That’s what has happened in your job, and if you look at the part of the log file dealing with the packing test, you should see some notification that this has happened.
Best wishes,
Randy Read
From: [email protected]
Date: Wednesday, 25 March 2026 at 06:32
To: [email protected]
Subject: [phenixbb] Monomer of dimer?
Dear PhenixBB community,
I am currently working on solving the structure of protein X (110 amino acids). The protein forms a dimer in solution, and dimerization is functionally relevant.
Based on initial analysis, the asymmetric unit (ASU) was estimated to contain one copy [unit cell: 82.699, 82.699, 36.435, 90 , 90, 120]. The data extend to 1.2 Å resolution, but the final R factors are around 0.23/0.25, which seem higher than expected at this resolution, and we have not been able to improve them further.
When I examined the structure using symmetry mates in PyMOL, I observed a clear dimer that appears biologically meaningful. This makes me suspect that the ASU estimation might be incorrect—especially for a small protein like this, the ASU could potentially contain a dimer rather than a monomer.
However, every time I use a dimer model as the search model for molecular replacement, Phaser consistently returns a monomer solution. I would greatly appreciate any suggestions on how to successfully obtain the dimeric model that matches the crystallographic symmetry.
Thank you in advance for your help!
Best regards,
Liu
_______________________________________________
phenixbb mailing list -- [email protected]
To unsubscribe send an email to [email protected]
Unsubscribe: phenixbb-leave@%(host_name)s
