I observed high solvent content as a warning from the phaser when I solve my structure. What's the cause of the high solvent in protein crystal?
p.s. I calculated the Matthew probability of my crystal, and it predicted it as a 10mer. I did MR with phaser using 2 copies of my model. Could this be why?
I'd suggest you try to first search for the suggested number of copies with the highest probability, unless you already know your crystals have a high solvent content. In your case, the program would complain about it if the suggested copy number is 10 but you input only 2 (solvent content would be >80%, I guess).
Dear Gengnan Li ,
probably you already sorted out this issue, but I'll weigh in any way.
You don't mention the resolution of the data. Bear in mind that at lower resolution and high solvent content, Mathews coefficient "trembles" a bit. Do not assume a 10mer straight forward, try to phase searching for 8 molecules, and then 9, and then 10, and so on. Eventually you'll reach a step where no more molecules are found.
Anyway, refine the solutions and check R/Rfee variation, and eventually FoFc(+) maps: is there additional blobs of positive density? If so, probably there are more molecules to search for. Also check, e.g. in PyMol, for crystal packing: are all molecules in contact with each other? Are there any "holes" in the packing? If so, keep searching.
One final hint: if you are looking for a 10mer in the ASU, and you give PHASER a 2mer, you have to look for 5 molecules. Probably PHASER is complaining because it calculates Matthews coefficient, it "guesses" 10 molecules in the ASU, and you have only asked for two molecules (you 2mer search model).
Hope this helps. Get back to me (in private if you want), if I wasn't clear eneough.
Best regards,
Jose
- Badges
- Science topic