Dear Jacob, An example where special efforts were made to investigate biocatalysis and the role of ions, harnessing both softer X-rays and ion substitutions and a WASP analysis to be sure as possible of their identity, can be found here:- http://www.ncbi.nlm.nih.gov/pubmed/20099851
The review article on metal atoms in proteins by M M Harding Crystallography Reviews 2010 http://www.tandfonline.com/doi/full/10.1080/0889311X.2010.485616 which I see just now has been downloaded 722 times thus far, should also prove instructive. I commend to you also the wiki:- http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Properties_of_proteins You indicate that oxygen anomalous scattering could be used; whilst this is applicable to chirality determination in small molecule organic crystallography the oxygen anomalous signal is very small and to my knowledge not used thus far in protein crystallography. Best wishes, John Prof John R Helliwell DSc On 6 Mar 2014, at 19:45, "Keller, Jacob" <kell...@janelia.hhmi.org> wrote: > Dear Crystallographers, > > I was curious whether there has been a rigorous evaluation of ion binding > sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine that > there is a considerably broad spectrum of habits and rigor in assigning > solute blobs to ion X or water, and in fact it would be difficult in many > cases to determine which ion a given blob really is, but there should be at > least some fraction of ions/waters which can be shown from the x-ray data and > known geometry to be X and not Y. This could be by small anomalous signals > (Cl and H2O for example), geometric considerations, or something else. Maybe > this does not even matter in most cases, but it might be important in > others... > > All the best, > > Jacob Keller > > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Farms Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: kell...@janelia.hhmi.org > *******************************************
