Dear All,
I would like to quantify electron density inside of positive Fo-Fc blobs in
active sites of multiple protomers in the map and compare them. I am aware
that I can interpolate maps and obtain density values at coordinate points
using either MapMan, Chimera or Coot, but I would like to
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Hello All,
I have run into something odd. In working on a structure for one of the groups
I work with regularly, on one of the cystine residues I have a very large
positive density peak at the sulfur position. The B value is approximately 4
times the other values in the residue and on other
A large B value with positive difference density sure implies a
convergence problem with the refinement. Was the B value extreme in
your starting model? (A starting B that is wildly too large or too
small at the start may cause it to become trapped in the refinement.)
Maybe if you rerun
Do you mean the sulfur atom density is larger, or do you mean there is a
density peak adjacent to the sulfur atom? It is possible for cysteine (CYS)
residues to be oxidized to S-hydroxycysteine (CSO) under certain storage or
crystallization conditions. Ran into this in a cysteine hydrolase
Thought of this originally but the peak is almost on top of the Sulfur and with
the oddly high B value I don’t think it is that. I would also think it would
show up on both monomers vs just one.
Len
On Aug 10, 2022, at 10:26 AM, Roger Rowlett
mailto:rrowl...@colgate.edu>> wrote:
Do you
The high peak is to be expected if the B factor is ludicrously too high.
I think the problem is in the behavior of the B factor refinement.
Try setting all B factors for the CYS to some sensible value (you can do
that in COOT - ) then see what happens after more cycles of refinement..
Eleanor
I wonder if the high B factor, - 4 times higher you mentioned, is consistent
with a sulfinic/sulfenic acid in rotation-so that the atoms dont appear
resolved. -The two molecules are definitely in different environments so that
even a small difference structure (or dynamics) there or access to
I've seen this happen with B-factor refinement reasonably often. As I
understand it the basic problem is that for small B-factors the gradient
d(density)d(B) is large, but for large B-factors the gradient is small. So if
the starting B-factor on an atom is very low and substantially lower than
It is possible that the cysteine residue in question got oxidized - the likely
products are sulfinic acid SO2H or sulfonic acid SO3H. Since the two molecules
in the asymmetric unit are in different environments one could be more prone to
the oxidation than the other. Alternatively reaction with
While the B value in the starting model was fine. I did drop it to a
reasonable value and it now seems to be behaving, was thinking about trying
that before I posted. Since this was an MR determination I did check and the
starting model B value was actually smaller then the surrounding
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