[phenixbb] question on molecular replacement

Machius, Mischa Christian mischa_machius at med.unc.edu
Mon Jun 11 06:19:00 PDT 2012

Besides what others said about the technical aspects of your molecular replacement endeavors:

Gel filtration is not the most accurate method to determine oligomeric status. Also, the content of the asymmetric unit may or may not have anything to do with the oligomeric status of a protein. So, best not to pay too much attention to that. First, try to find four copies, then another one, if there is still space and there is electron density indicating another molecule.

More importantly, designed structures often deviate significantly enough from 'real structures that molecular replacement becomes difficult or impossible. There is great satisfaction to be derived from a designed molecule being suitable as a search model in molecular replacement, but in the end you'd really want an independently determined structure. I assume that part of the motivation behind determining the crystal structure of your protein is to verify your design. If so, a completely independent structure would be desirable and would also convince any reviewer. Thus, I would recommend generating the seleno-methionine variant of your design (provided it contains any methionines) and solving it experimentally.

Best of luck!

On Jun 10, 2012, at 10:57 PM, <fn1 at rice.edu>

> Hi everyone,
> I have a dataset in P21221. The cell content analysis shows that there should be 5 monomers in asu. The gel filtration profile of this protein shows that it should form a tetramer.
> I have a simulated structure as searching model. I try to use the whole model or backbone model, and different resolution cutoff. When the whole model is used, the llg of solution is negative. When the backbone model is used, the llg is about 160 when searching for 4 monomers and tfz is 7.4. But the following autobuild process could not lower rfactor than 50%.
> I notice online that it might be useful to run self rotation function first to find ncs operators before doing mr. Is this true and how can i do this?
> Thank you in advance!
> Fengyun
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list