The funny thing is, although we generally regard resolution as a primary
indicator of data quality the appearance of a density map at the classic
"1-sigma" contour has very little to do with resolution, and everything
to do with the B factor.
Seriously, try it. Take any structure you like,
Looks to me like those two waters are just close enough to push the bulk
solvent mask out of that region. Have you tried optimizing your bulk
solvent parameters? (keyword "solvent optimize" in refmac;
"optimize_mask=True" in phenix).
Also, try exporting your bulk solvent mask (MSKOUT in
Hello Jessica,
options to test (in order to judge what is going on in the active site):
1) Take all the water/ion molecules out of the pocket and refine the
rest of the structure as good as you can (without overfitting
everything) and calculate a sigma A-weighed *3Fo-2Fc* map. Since you
Chloride coordination spheres are typically tetrahedral (CN=4) or square
pyramidal (CN=5), and occasionally octahedral (CN=6). Arg and His and well
as amide nitrogens are common protein ligands, and it is possible but not
common to see carboxylates in the coordination sphere.
Roger Rowlett
On
hey Jessica
a tip that might come up later on anyway: once you put every reasonable bit
into the desity, what I like to to when facing such blobbs: I take a well
defined water out to create a diff density at a position where I know it is
real. Having a feeling of how much you have to contour
In addition, one should carefully consider the chemistry and coordination
geometry around the putative chloride ion. Not only do candidates have to
be consistent with the observed omit density, but they must also make
chemical interaction and geometry sense. I suspect a partial occupancy
water may
Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without placing
anything in the unclear blob of your interest so to obtain the best
possible phases and hopefully improve the blob density as well.
Then you should let the
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