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:[log in to unmask]] On Behalf Of Hubing Lou
Sent: Thursday, July 21, 2011 6:46 AM
To: [log in to unmask]
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