Hi Ed -
There was a peak in the difference maps, as I recall. I believe it
initially got built as a water, but that proved to be too many
electrons, giving a negative peak. I removed the water, but it was
clear that something needed to be there, at which point I started
casting about for alternative atoms, and settled on lithium. I'm pretty
sure I never tried to put sodium in there and see if it refined.
Caveat: this work was all done eight years ago, and I don't have access
to any of the files anymore. So I can't verify any of these
statements! However, I did deposit Fobs for these structures, if you
care to make your own maps...
I just checked the structure in EDS, and the peak for the lithium is
pretty low, around 0.6 sigma. I would say that it looked better in the
maps I was using.
Hope that helps,
Matt
On 1/12/12 11:22 AM, Ed Pozharski wrote:
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
--
Matthew Franklin, Ph. D.
Senior Research Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(646) 275-7165
