Structure Refinment problem

From: Muhammed bashir Khan
Date: 19 February 2012 18:38


Dear all;

I have a structure at 3.3A resolution of about 140kDa protein containing
eight domains, in tetragonal space group.I also have the structure of most
of the individual domains.I almost refined the structure in all the
possible space groups, the best space group at the moment are the P42 with
the R/Rfree of 32 and 38%. Could somebody suggest what else I should try
to to get better R/Rfree values. I am using Phenix for refinment.
Regarding the protein it contain quite flexible domains.

Thanks in advance for your suggestions.

Regards,

Bashir



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From: Bosch, Juergen

I don't see a real problem, you seem to be doing the right thing.

Check out the Molprobity server and see what it suggests to improve on your structure.

You could run pointless to verify that P42 is the true space group but looking at your ∆Rfactor of 6% you likely have the right solution.

Do you have one monomer with eight domains in the asu our do you have more than one copy? If so then identify the regions which follow NCS and apply them.

Jürgen

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From: Pavel Afonine

Hi Bashir,

the R-factors seem to be hight given the resolution. I don't know what you have tried so far and what you haven't, and the list of things to try is too long. It might be more efficient If you send me the data and model (off-list), so I have a quick look and may be suggest something.  

Pavel