[phenixbb] Problem with molecular replacement

Randy Read rjr27 at cam.ac.uk
Thu Apr 9 01:30:25 PDT 2020

Dear Shramana,

I may be reading this incorrectly, but it sounds like you’re providing the entire PDB file from the solved model to Phaser to solve the other structure by MR.  You need to edit the PDB file before using it as a model so that what you have is a sensible model for what is in the other crystal form, because Phaser will just take the whole thing as a single rigid body.  Given the 100% sequence identity, I would use a single copy as a model and search for the appropriate number of copies (perhaps 4, from what you say).  If the model was more distant, then it might be worth looking at it to see if it could plausibly be a dimer or tetramer in solution, and then you could use a higher-order structure.  But MR with identical models can usually place a reasonable number of copies independently, and then you don’t have to make any assumptions about quaternary structure.

Best wishes,

Randy Read

Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research     Tel: +44 1223 336500
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> On 9 Apr 2020, at 04:43, Shramana Chatterjee <schatter90 at gmail.com> wrote:
> Hi,
> I am trying to solve a structure using a data solved by SAD as an reference (ensemble in phaser). The structure I am trying to solve has 100% sequence identity with the solved one. The problem that I am facing during Phaser MR is that, in the solved structure there are 6 molecules in the ASU although I am getting maximum 4 molecules in the ASU and also Rfree is around 0.49 just after the phaser. Phaser is showing a good values of LLG (>500) and TFZ (>8).
> It would be very helpful if I get any suggestion about the above-mentioned problem.
> Thank you in advance.
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