Dear TriNigo
I would put waters in all the other difference density first (there
are several obvious waters even in the section of map you sent with
your email), without the substrate, and see if you see any more clues
as to what's going on. Do you expect something to be added on the
substrate in the reaction? Could you be looking at product?
Regards
Christine
Dear ccp4 experts,
I am trying to solve the structure of one esterase with its
substrate. The structure was solved by MR to the resolution 2.2 A.
In the active site, I can see clearly the different density map of
the substrate (S- methyl hydroxy isobutyrate). After puting the
substrate into that density map, I use Refmac to run restrain
refinement at 0.1 weighting term.
Even though the substrate fits to the different map very well, a
big different map appears at one end of the substrate after Refmac
refinement. I attach the image so that it's easy to see the problem.
I tried to put water or Na (because the crystallization contains:
1M sodium citrate, 100mM Na Cacodylate, 20% glycerol) but it didn't
work.
I tried to use CNS instead of Refmac, however the result is worse
since the R-free is increased and the different map is still there.
Because I am new with CNS so I don't know which parameters I should
adjust.
Do you have any suggestion to solve this problem? Thank you very
much for all of your helpful advice!
My best regards,
TriNgo,
PhD student,
Sungkyunkwan University, Korea<esterase_mut_S_ligand.png>
