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Dear Matt,
95% solvent is highly unlikely, but not impossible. Did you have a look at the crystal packing? Are there continuous crystal contacts in all three
dimensions, or are there layers of molecules that are not connected? Are you sure your space group is P212121 and not one of the other seven P2x2x2x space groups? You have to test all possible space groups. With presumably so many molecules in the asymmetric
unit, you may have non-crystallographic symmetry mimicking crystallographic symmetry.
If you are sure you have used the correct space group and you have a decent resolution (say better than 2.5Å) you could also try to just refine
your solution and see if some density for the missing molecule(s) appears.
Good luck!
Herman
Von: CCP4 bulletin board [mailto:[log in to unmask]]
Im Auftrag von Matthew Bratkowski
Gesendet: Freitag, 16. Mai 2014 00:51
An: [log in to unmask]
Betreff: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular Replacement
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