Dear Hubing,
One maybe stupid question: Your are sure the space group is P21 and not
P2 or even something else? Did you test other possible space groups?
Choosing the wrong space group could exactly lead to the results you
observe.
Best,
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Hubing Lou
Sent: Thursday, July 21, 2011 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phaser and Molrep gave different solutions
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. 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
