[phenixbb] Different cell content than expected in Xtriage

[Singh, Bishal]

Dear Folmer,
 Thank you very much for your words. Yes! I refined the model after molecular replacement. Electron density is nicely defined for all residues including their side chains. There is no extra electron density. All refinement parameters are fine. Rwork and Rfree are around 22% and 25%, respectively. The model  that I used for phaser was a homology model generated from a structure with 60 % sequence identity to my protein. I prefer to use homology model than providing sequence identity in phaser because I think that the local structural errors are more precisely defined in homology models.

Thanking you again!
Kind regards,
Bishal

From: Folmer Fredslund <folmerf at gmail.com<mailto:folmerf at gmail.com>>
Date: Tue, 18 Aug 2015 15:34:23 +0200
To: noro <b.singh at dkfz-heidelberg.de<mailto:b.singh at dkfz-heidelberg.de>>
Subject: Re: [phenixbb] Different cell content than expected in Xtriage

Hi Bishal,

Did you try to refine the model from phaser?
Did you check the packing of the 2 molecules?
Did you look at the electron density from phaser and see if some of it could look like an extra molecule?


It is not impossible to have 70% solvent content, so I don't think you should be too worried, just investigate the result.
You probably have another molecule there, phaser was just not able to find it, but you should be able to manually fit it easily.

Btw, how similar is your model to your own protein?

Hope this helps
Folmer Fredslund

2015-08-18 15:02 GMT+02:00 Singh, Bishal <b.singh at dkfz-heidelberg.de<mailto:b.singh at dkfz-heidelberg.de>>:
Dear all,
  I am solving crystal structure of a protein of size 33.7kDa in space group P 43 21 2 at 2.25 Å resolution. Unit cells constants are 121.51 121.51 156.6 90 90 90.

The cell content analysis in Xtriage showed 1050 residues (~ 3X 33.7 kDa) per ASU with 50 % solvent content, whereas the molecular replacement in mr-phaser produced a dimer (2X 33.7 kDa). When we consider a dimer per ASU, it should have approximately 70 % solvent content. Please suggest me whether solution is right or not. I shall appreciate your opinions.

Kind regards,
Bishal

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Folmer Fredslund