Peroxyacids are unlikely - they're very reactive/unstable under normal conditions. Is it possible your crystal is just at unusually low pH so these acids are protonated? That makes the carbon-oxygen bond lengths asymmetric, possibly by enough to explain your blobs.
Tristan Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 3 May 2017, at 05:29, Edward A. Berry <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 > <peroxyglu1.gif> > <peroxyglu2.gif> > <peroxyglu3.gif>
