Re: [ccp4bb] bond lengthening in atomic resolution structure

2009-09-16 Thread Brad Bennett
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 determi

Re: [ccp4bb] bond lengthening in atomic resolution structure

2009-09-16 Thread Dale Tronrud
To judge the significance of the value of a bond length, you cannot rely on global measures of precision. You need the standard uncertainty of this particular distance in this particular crystal. Refmac will not perform this calculation for you. Shelxl will. It is certainly more cumbersome t

Re: [ccp4bb] bond lengthening in atomic resolution structure

2009-09-16 Thread Ethan Merritt
On Wednesday 16 September 2009 11:19:11 Ivan Shabalin wrote: > 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 >

[ccp4bb] bond lengthening in atomic resolution structure

2009-09-16 Thread Ivan Shabalin
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 o