Re: [ccp4bb]: Unexpected negative density on ligand N

[Anastassis Perrakis]

Yet another relatively wild guess, since as you say the problem is close to a non standard aa, is that if one of the neighboring residues in either side ofth peptide bond under investigation is D- instead of L-, this can cause little changes in modeling. These together with trying to keep the whole of the geometry tight to L-, at 2.2 might show up as negative density in the N atom. In other words you might be seeing an effect due to incorrect modeling that is not the actual problem. I had a similar case, were finally I was modeling L- instead of D-  ... or R- instead of S- as our chemist guru explained to me, since we did not actually measure the optical activity of the aa analogue ;-) but that was at 2.9 and became clear at 2.4 ... a similar explanation might apply if you are dealing with a Cis-peptide bond. ... or of course you might have one atom too many. ;-) A. On Jul 10, 2006, at 14:03, jean wrote: I asked the organic chemist who synthesised this ligand and he assures me there is no way the atom could be anything other than a N.  My only other thought is perhaps this atom is different, in terms of electrons, from a typical peptide N?   It's the peptide bond before the ligand C-terminus.  Also the ligand is not a true peptide: the N of the previous peptide bond (to the N-terminal side of the problematic one) has been replaced by a C and the adjacent carbonyl group has formed a gem-diol at the active site zinc ion.  The offending N and the gem-diol are separated by two CH2's and a carbonyl group.