On 07/21/2011 01:45 PM, Hubing Lou wrote:
> Dear all,
>
> I am stuck in a molecular replacement case and looking for advices.
> I have been working on a protein-DNA complex structure.
> Data was processed by HKL2000 to 2.6Ang and some of the data statistics
> are shown below:
>
> Space group: P21,
> Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90
> Redundancy: 2.8 (2.7)
> Completeness: 94.8 (93.1)
> Linear R-fac: 0.051 (0.442)
>
> Data quality was checked by Phenix.xtriage and there's no problem. I
> then prepared a model by Chainsaw. Our protein shares only 30% of
> sequence similarity with the model, but structurally they are in the
> same group and almost identical in apo form. Matthrews Coeff indaced two
> monomers in AU. I then ran Phaser in "automated search" mode and there's
> a solution with RFZ score 4.8, TFZ score 3.8.
Hi,
Isn't this a bad sign usually when the TFZ score is lower than the RFZ
score?
Regards,
F.
> The electron density map
> was not bad with DNA double helix clearly seen. However Refmac5 couldn't
> get Rfree lower than 50%.
>
> I then changed to MolRep, ran "self rotation function" first then used
> the first 10 peaks for translation search. Again there's a solution but
> it is different from that from Phaser. I attached a picture here.
> Checking in coot, the packing is the same. But, the refinement couldn't
> get Rfree lower than 50%.
>
> I have tried to include NCS, TLS refinement in Refmac, both not working.
> Hope someone out there can help.
> Thanks very much for your time.
>
> Hubing
>
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