Hi, Although it's pretty much true that if TFZ>8, the solution is correct, there are hard cases where a correct solution has a significantly lower TFZ score. Also, we've been finding that TFZ scores are generally lower for monoclinic space groups like P21, at least in the search for the first molecule. (Among other things, the search for the first molecule in a polar space group only covers a plane, so there are fewer independent trials.) Rob Oeffner has been doing some detailed statistics, which we're analysing so that we can give better rules of thumb. However, a TFZ of 3.8 for the second molecule (where the search is 3-dimensional) is a bad sign.
One of the earlier posts suggested looking just for the DNA, which sounds like a good idea. It's possible that the relative orientation of the protein and DNA is different enough that the complex model doesn't work, so it might well be worth trying the DNA and protein components separately. Good luck! ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 21 Jul 2011, at 11:39, Hubing Lou wrote: > 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 > > 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 > > > ------------------------------------------------------------------------ > > > >
