Dear Alex,
Sorry yes I was focussing on the crescent density, since I imagined
the metal atom assignment was secure. SInce Zn and Fe are now
mentioned you would need to consider a tuned Xray wavelength anomalous
experiment to be sure it is nickel, although the circumstatial
evidence looks promising already.
Re the series termination effects; see eg:-
A. Minichino, J. Habash, J. Raftery and J.R. Helliwell “The properties
of (2Fo-Fc) and (Fo-Fc) electron-density maps at medium-to-high
resolutions” (2003) Acta Cryst D59, 843-849.
and references therein.
That said my main idea of a cause of the crescent density being due to
severe ice rings is not the case, as you now describe, so I am not
sure what causes what you have there around your nickel ions.
Greetings,
John
On Thu, Feb 24, 2011 at 5:02 PM, Alex Singer
<[log in to unmask]> 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
>
--
Professor John R Helliwell DSc
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