An additional information would be to calculate an anomalous difference
map: at typical synchrotron wavelenght of ~1 A, Ni would have ~2
electrons f'', whereas Cl would have only ~0.2 electrons f''. So, a
strong anomalous difference density peak would be more consistent with
Ni than with Cl.
However, if the data set was collected on a home source with CuKalpha
wavelength, such a map would be not be very helpful here, because the Ni
signal is about as weak as the Cl signal.
Best regards,
Dirk.
Am 24.02.11 16:37, schrieb Gloria Borgstahl:
I'm voting with Roger this time.
If I were you I would model a nickel in there (unless you have a
better candidate)
if it is right, the distances to the His should be like seen in a SOD
active site.
Then you can model the bonds and waters. You may need partial
occupancy on the metal.
Reminds me of the time I found a 6th water in MnSOD as I was
making the token electron denisty
figure of the active site. Found myself doing more refinement and a
much better paper.
On Thu, Feb 24, 2011 at 8:15 AM, Roger Rowlett <rrowl...@colgate.edu
<mailto:rrowl...@colgate.edu>> wrote:
This looks suspiciously like a metal ion with 3 or more resolved
water ligands. It's hard to tell from the images provided, but it
looks like the metal could be close to octahedral, with 2 His and
3 water ligands well-defined. The estimated metal-nitrogen bond
distances might help narrow down the metal ion. For example,
tetrahedral Zn(II) has a Zn-N bond distance of around 2.0 A. I
suppose this could be a Mg(II) ion, since that is in your
crystallization mix, but I think that Mg(II) typically prefers
harder protein ligands, e.g., carboxylates. Zn(II) is a very
common contaminant in solution, however, and should not
necessarily be discounted; indeed Zn(II) and other first row
transition metal ions would be expected to have a reasonable
affinity for medium hard/soft ligands such as vicinial His residues.
Cheers.
On 2/23/2011 7:34 PM, Alex Singer wrote:
cocrystallized in 2.5mM Glycero-3Phosphocholine and cryoprotected
by dipping in
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