Alex,
I modeled in the bis-tris with the tertiary amine and and his
imidazole coordinating axially and the four oxygens coordinating in
the equatorial plane. However, it's hard for me to tell from your
images if there are two His coordinating? Either way, that crescent
shape could easily be explained by a bis-tris molecule, you'll just
have to figure out how exactly to model it in. It's also possible that
the metal is a Mg, but as people have already mentioned, nitrogens
probably wouldn't coordinate very tightly to a hard metal. Lastly, I'm
also not sure off the top of my head how tightly bis-tris binds
metals, but it should be an easy number to look up. Hope this helps,
Jeff
On Feb 24, 2011, at 9:02 AM, Alex Singer wrote:
> Hi -- thank you for all your help. The majority opinion seems to be a
> metal for the sphere (Ni from the Ni-affinity column, which (Joe
> Patel, correct) was used during purification, but Zn and Fe were also
> mentioned), and either water molecules, bis-tris or some other small
> molecule forming the crescent. Just looking at the density, the
> occupancy would seem to be quite high, so I'm surprised that a Ni ion
> (or a contaminating metal ion) could have gone through the
> purification and still remained at high enough concentration to be
> clearly visible in the crystals. However, I'll still try this but
> first some points of clarification and questions which you can either
> email me seperately or post to the the group.
>
> a. it was collected at beamline 19-BM at Argonne, so radiation damage
> is an issue. Thierry Fishmann -- for the gln residue, there was
> difference density for the gamma carbon after the first conformation
> was modeled in, thus the addition of the second conformation, which I
> agree is suspect. What does the radiation damage do chemically and
> would that make the gamma carbon more mobile?
>
> b. Jeffrey D Brodin -- how did you model in the bis-tris? Looking at
> the bis-tris molecule from Hic-up, was the N at the centre of the
> crescent and the O6 and O8 at the edges?
>
> c. JR Helliwell -- there are 4 molecules in the AU, but two H138's
> are pointing into the solvent. Thus the molar ratio of protein
> molecules to "thing 1" is 4:1. Also looking at the images, I see no
> ice rings -- the images look pretty good. Can you tell me more about
> the series termination effects?
>
> Again thank you for your help and I'll let the group know how it
> worked out.
>
> Alex
>
> --
> Dr. Alex Singer
> C.H. Best Institute
> 112 College St. Room 70
> University of Toronto
> Toronto, Canada, M5G 1L6
> 416-978-4033
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