Matt,
thank you, this is an excellent summary. One question remains - the
lithium peak should be, afaiu, much lower than the water/sodium. Was
there a peak in difference map or was placement based on identifying
something that looked like a coordination site?
Cheers,
Ed.
On Thu, 2012-01-12 at 10:23 -0500, Matthew Franklin wrote:
> On 1/12/12 9:42 AM, Ed Pozharski wrote:
> > On Thu, 2012-01-12 at 09:52 +0000, Patel, Joe wrote:
> >> Do you have ultra-high resolution? Something I did not…. Are there
> >> many examples in the pdb of proteins with Li+ refined?
> > http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI
> >
> > 39 in total. Some are fairly low resolution (2.8A), and only five are
> > higher than 1.2A. I'd think that placing lithium ion should be based on
> > some extra-crystallographic evidence, plus maybe some structural
> > considerations such as correctly placed coordinating ligands.
> >
> Since I'm responsible for eight of those structures, I'll just say that
> I thought fairly hard before building a lithium into that peak, knowing
> that I couldn't really distinguish it from water or sodium. I was
> working with a 1.7 A map, and I put the lithium there based on three
> criteria:
>
> - the crystals grew in something like 2 M lithium sulfate, whereas the
> only source of sodium would have been from the buffer or the protein
> solution
>
> - there were two negatively charged residues coordinating the peak in
> question, suggesting it was a cation
>
> - the bond distances were consistent with lithium coordination, for what
> that's worth at this resolution
>
> That was the first structure (1TW7), and all of the others were treated
> the same since it was the same crystals soaked with different compounds
> in the same conditions.
>
> - Matt
>
>
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
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