You haven't given much detail to work with so I can only guess about your problem. A Wilson B of 20 for a 4 A data set is ridiculous, but the uncertainty in the Wilson B calculation at 4 A is enormous, so what might be a more reasonable statement would be to say your Wilson B calculates to 20 +_ 300 A^2 and the true value would be in that range. I don't think a precise Wilson B is important for MR so I wouldn't worry about it.
An R value of .7 after MR is very large. Its size implies a systematic problem with your model - I would be looking for a second monomer. You haven't said anything about the structure of your monomer. Often a ligand will bind in the cleft between two domains, and the domains move relative to each other upon binding. You may have to perform separate searches for each domain or construct a range of trial models with different angles between the domains. Don't worry about the ligand until you solve the protein structure. Whether you see it in the end will depend on how big it is and how good your 4 A data are. Of course, it's possible that it doesn't bind at all. Dale Tronrud On 06/07/10 12:17, yang li wrote: > Dear colleagues, > > We are now trying to soak some ligands into a protein, which is > about 60kd in size and the structure has been solved > before. But the molecular replacement cannot give a right solution. > Below is some contrast of the data: > > Native 2A P212121 monomer > Soaked 4A F222 monomer (more than 70% solvent) or > dimer(more possible) > > I wonder if it is possible to find the ligand in the case of such low > resolution, provided the ligand is not so small. What facts > could probably lead to the failure of MR? Molrep gave a model of monomer > but the rfree is as high as 0.7, while phaser could > get no result. I tried phenix.explore_metric_symmetry to find the two > spacegroups are not compatible, and the Rmerge of the > data seems reasonable. > One more question is: the wilson B of the data is lower than 20 from > ccp4. Is it common for a 4A data? Since I donnot have > the experience of handling this low resolution data yet. > By the way, any suggestions about refinement methods in low resolution > will be appreciated! > > Best wishes > Yang
