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
