This appears to be a symmetry threefold axis. These areas are notoriously prone to have density artefacts. Also it looks like your terminal carbons are pointing in the opposite way, and the entire end of Met is slightly shifted as a result. You may never be able to fit this area to your satisfaction - due to the symmetry axis. I would definitely experiment with allowing partial overlap - remove steric restraints on this residue so they don't bump into one another then see how the density looks - if things return to normal - perhaps you're forcing a close collision - maybe there is a small error in unit cell parameters for instance, etc.
Artem > > Dear all > > I am doing one structure at 2.6A resolution where I found unusual density > near methionines. Actually three methionines come close together nearby > and I get difference even at 5sigma cutoff. I don't understand nature of > the density. The amino acid sequnce is same I mean met by chemical > sequncing so there is no change amino acid residues. I am sending the > snapshot of the difference fourier observed at methionines. The crystal > belong to R32 system with one molecule and biological trimer. In snapshot > two of the methionines are symmetry related. > > Details of the data collection. > Data collected at synchrotron > > Overall Rsym = 6 % and I/sigma = 2.1. Completeness = 99% > > Can anyone suggestion what could be chemical nature for the difference > fourier. > > Thanks in advance > > Ethayathulla > > ################################################### > A.S.Ethayathulla,Ph.D. > Department of Biophysics > All India Institute of Medical Sciences > Ansari Nagar > New Delhi-110029 > India. > ################################################### >
