Hi Ivan- Since you most likely have the data to back it up and I assume you have the computational firepower to do it, why don't you run a full matrix refinement in SHELX to get estimates of bond lengths and their deviations? It's worked for me in calculating carboxylate C=O bond lengths to determine charged vs. uncharged Asp residues.
Best- Brad 2009/9/16 Ivan Shabalin <shaba...@inbi.ras.ru> > Dear all, > > I have an atomic resolution (1.1Å) structure of enzyme with the bound > cofactor NAD. During the analysis of the refined structure I found that > important double C=O bond of the cofactor in the active site was slightly > lengthened from standard 1.22Å to 1.26Å. Then I increased the > sigma's of the > distance restraint in the REFMAC dictionary 50-fold and as a result the > distance increased to 1.29 Å. I suggested that this deviation from > standard > double C=O bond means decrease in the bond order to something between 1 and > 2. This change in bond order upon cofactor binding (and especially in the > transition state of the reaction) was suggested previously by studies of > the > kinetic isotope effects and partly confirmed by quantum mechanics > calculations. > > This change in 0.07Å is quite small, but is a bit higher than the DPI > multiplied by a factor of two (2*0.028=0.056). Is it crystallographically > sound to state the bond lengthening? Is DPI the correct estimation of error > of positional parameters in my case (note that B-factors in the active site > are about 12-15, when average B-factor for all atoms is 20)? Maybe, ML > based > su of positional parameters is better estimation. > > Statistics of the dataset (values in parentheses are for the > highest-resolution shell 1.11-1.10 Å): > R-merge = 5.1 (52)% > Redundancy = 4.0 (2.5), > Completeness = 96.5 (73.8)% > <I>/<σ(I)> =44 (1.9), > mosaicity = 0.7 (I think, this value is a little bit high). > > Statistics of the refinement with REFMAC: > R-factor =13.4% > R-free =15.9%, > RMSD_BOND = 0.015Å > DPI = 0.028 > ML based su of positional parameters = 0.0217. > Estimated with SFCHECK maximal error 0.062 A > Estimated with SFCHECK minimal error 0.014 A > > All help greatly appreciated!! > > Yours, > Ivan >
