Have you tried fixing the molecule that looks correct and searching for others? You might have greater than one but less than 9 molecules per ASU.
When you do this, try imposing severe restraints on the packing function. This worked for me in Phaser with a difficult case. My anecdotal experience is that, when you have lots of molecules per asu, the correct solution gets swamped by poorly-packed solutions if the default packing penalties are used. Good luck. Sent from my iPhone > On May 15, 2014, at 6:50 PM, "Matthew Bratkowski" <mab...@cornell.edu> wrote: > > Hello all, > > > I am working on the structure of a small protein in space group P212121. The > protein is monomeric in solution based on gel filtration analysis. The > Matthews Coefficeint program indicates that 9-10 molecules per asymmetric > unit results in ~50% solvent content, while 1 molecule per asymmetric unit > results in ~95% solvent. > > I tried molecular replacement with a search model which is essentially > identical in sequence to my protein, and searched for 9 or 10 molecules/asu. > Using MolRep with 9 or 10 molecules/asu, I get poor contrast scores around > 1-1.5. However, when using Phaser, I get a solution with one molecules/asu. > Likewise, when I went back and tried MolRep with 1 molecule/asu, I got a > contrast score of 3.12. This model still has some issues, but looks more > correct compaired to models created with 9 or 10 molecules/asu. > > It seems highly unlikely that a crystal would contain 95% solvent, but is > there any possiblility that this could be the case? Assuming that the > Matthews coefficient is correct, does anyone have an idea why MR seems to > work better for 1 molecule/asu with 95% solvent content compared to 9-10 > molecules with 50% solvent content? Alternatively, is there any reason why > the Matthews coefficient could be calculating incorrectly? Any suggestions > would be helpful. > > Thanks, > Matt
