How about disorder and/or partial occupancy? B-factors of the Thr and Cl seem pretty high compared to the rest of the structure.
Hydrolysis during (possibly weeks/months of) crystallisation is another option. Check the pH and presence of nucleophiles. cheers, Hans Mike Gretes schreef: > Hello, > > Does anyone have any insights into close intermolecular contacts > involving Cl atoms in crystal structures? There may be some basis for > close contacts (~ 2.5Å) in the phenomenon so-called halogen bonding > [ref-1] but this does not explain close C-Cl contacts observed in some > structures for example (among many): > > 1XVF - monomer B: Thr213-O-gamma - ligand Cl > > In this example, there seems to be very weak electron density for the > Cl atom (and indeed a negative difference map peak at 8 sigma). 2HVX > (for example; and a number of others) have a ligand Cl at a difference > map peak -6 sigma. Are these simply poorly modeled/poorly supported > by the experimental data? Radiation damage? Or does anyone know why > Cl atoms would scatter poorly (for some reason that I cannot imagine)? > > Thank you for your input. > > Mike Gretes > PhD Candidate > University of British Columbia > > [ref-1. Lu et al. Ab initio investigation of the complexes between > bromobenzene and several electron donors: some insights into the > magnitude and nature of halogen bonding interactions. The journal of > physical chemistry A (2007) vol. 111 (42) pp. 10781-8] > >
