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
