I was worried as well with the low TFZ score. Usually successful cases with score >8. I am still puzzled why Phaser and Molrep gave different solutions. Does this mean molecular replacement do not work out in this case so more crystals have to be prepared?
A little more information might be helpful to dissolve the problem here. The model I used is a protein-DNA complex. The protein was Chainsaw editted but the DNA sequence was directly borrowed from the original model. Best, Hubing On Thu, Jul 21, 2011 at 3:30 PM, Vellieux Frederic <frederic.velli...@ibs.fr > wrote: > Hi, > > It's not a bad idea to read the Phaser manual for molecular replacement; > see > http://www.phaser.cimr.cam.ac.**uk/index.php/Molecular_**Replacement<http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement> > > Soon after the start, in a table on the right hand side, there is: TFZ > score < 5, have I solved it ? No. > > Hence with a TFZ score of 3.8 you do not have a solution using Phaser. > > Fred. > > 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. 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 >> >> >> ------------------------------**------------------------------** >> ------------ >> >> >> >
