The total number of electrons in the two systems is identical, so you are
looking for that extra fraction located closer to S than to P due to the change
in atomic number.
I haven’t checked but I doubt if this is easy even in ccdb, and I would be
stunned if it is possible in the pdb. There might
Let me clarify. I was thinking not of the anomalous but of the regular 2FO-FC
density, which should be easy enough to quantify and compare to the relative
heights in thousands of high-resolution PO4’s and S04’s in the PDB. One could
even get a pretty good estimate of the likelihood the unknown’s
Besides the anomalous difference peak which might be similar in height to
the anom diff peak from an intrinsic sulfur found in cysteine or
methionine, also consider hydrogen bonding.
In general, a sulfate will not be donating a hydrogen bond. A phosphate
probably will.
##
Well - I try to quantify the relative anom peak heights by checking those
over MET or CYS S sites with similar B values v the disputed one.. The
expected difference between P and S isnt very big, but it might give you a
crystallographic clue.
Eleanor
On Sun, 17 Feb 2019 at 17:31, Keller, Jacob
Shouldn’t it be possible to look at the ratio of peak heights of O’s versus S
or P to figure out which is more likely? The must be thousands of examples in
the pdb with which to determine the ratio, even if one restricts the analysis
to “high resolution” structures.
JPK
+++
Hi!
As suggested below sulfur/phosphorous anomalous difference Fourier density
would be nice, but you might be able to figure out what's going without
collecting more data. Have you investigated the direct interaction partners of
your mystery oxyanion? Unless you are at extreme pH values, phos
Hi Shijun,
I had a similar issue a while ago that a acetylated lysine binding site was
occupied by acetate from buffer. In this case, I would suggest trying
crystallize in a conditions without SO4, e.g. using NH4Cl instead, if it is
reproducible.
Best,
Yu
From: CCP4 bulletin board [mailto:CCP
Dear all
Thanks for all your suggestions. PO4 is from my Ligand PI3P, but I cannot see
the electron density of the PI3P tail, and the binding site is exactly there.
While my crystal buffer salt is 50mM (NH4)2SO4, so I am afraid the SO4 occupied
the PO4 position.BTW, I can see the other SO4 ele
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