For P212121, I would put money on something divisible by 2 for the total
molecules per asu. Anything from 6-12 might be likely. One of the early
structures I worked on had 6 molecules per asu, which was darn near
impossible to find using momomers (at the time). The way it was
eventually solved was by finding a reasonable tetramer solution, then
looking at the packing of that model to see what was missing and
determine how much more would fit into the asu. Turned out to be another
(obvious) dimer, which did the trick. The Matthews coefficient predicted
something like 9 molecules per asu, which was not close to the actual
answer. When n=large number, the Matthews coefficient does not easily
identify a unique, most likely solution, but a range of reasonable
solutions.
One possible strategy would be to look for some partial solutions to
give you a better clue of the actual packing in the asu. If you find
there is a reasonable looking dimer pair, try searching with multiple
dimers, etc.
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 5/15/2014 8:29 PM, Toth, Eric wrote:
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
