Thanks to all who replied. Yes, in some of the other cases density between Cd and Cg is conspicuously weak. From preliminary tests it looks like dual conformations, in some cases together with correlated waters, will account for the density adequately. No Zebras here! eab
On 05/03/2017 04:26 AM, Matthew Merski wrote:
Have you tried just a double conformation of the Glu? Its hard to tell in your pictures but it looks like there might be less than perfect density for the CG-CD bond? If you just try adding a second conf of the Glu that might work too (and perhaps be a horse rather than a zebra making your hoofprints?) Matthew Merski Crystallochemistry Laboratory Univ. of Warsaw On Wed, May 3, 2017 at 6:29 AM, Edward A. Berry <ber...@upstate.edu <mailto:ber...@upstate.edu>> wrote: I'm finishing up refinement of a 1.8A structure (R's 0.17, 0.20) , and among the largest peaks in the difference map are small spherical blobs that seem to be attached (1.46 A here) to carboxylate O's (Figures). Are these likely artifacts? If not, how can I interpret/model them? One idea is that the acid has reacted with peroxide from the PEG to make the (hydro)peroxy-acid. I don't know how stable that would be, and I don't see any peroxyglutamate in Ligand Depot or HIC-Up. Another guess would be acid hydroxamate but I don't know how that would be generated. Methyl ester seems to be ruled out by the proximity of the two water molecules (2.45 and 2.48 A here) suggesting the mystery atom is an H-bond acceptor or donor. However since the occupancy seems to be < 1, the waters may be there only when the atom is not. I guess another possibility is there is a lot of motion in the plane of the carboxylate (up and down here) which cannot be modeled by my isotropic B-factors. In some cases the green blobs appear on both sides of the carboxylate (but that could also be alternate conformations of peroxyglutamate). The difference map (mFo-DFc, green) is contoured at 3 sigma (.06 e-/A^3). The difference peak is 5.4 sigma (0.1 e/A3). The 2mFo-DFc map is contoured at 1.5 sigma (0.1 e/A3). 2mFo-DFc density extends to the difference peak if I contour down at 0.64 sigma (0.04 e/A3, third figure). If I put an O atom there, link it with plenty of slack, and refine occupancy, it goes to 1.54 A from the carboxylate O and refines to occupancy 0.35, B-factor 15 (carboxylate O is 30). Now it is reached by 2mFo-DFc density at 1.5 sigma (0.1 e/A3). Any suggestions would be welcome. eab
