Given the average resolution of protein structures, reliability of ion site identification is almost always in question. Realistically, I think that only a combination of approaches and evaluation of several factors (including other experimental methods) leads to good answers (as I am trying to teach in my lectures). Therefore also an easy and uniformly reliable evaluation of ion sites in the PDB is not possible (too many details to be included in the analysis which are not part of the PDB record). In many cases though it is fairly easy to say "wrong ion".
Jan Dohnalek IBT Prague On Fri, Mar 7, 2014 at 7:09 AM, Robbie Joosten <[email protected]>wrote: > Dear Jacob, > > There are a lot of potential problems with ion validation, that make > obtaining a reliable answer difficult. If you want to datamine ion > validation results, you can use the ready-made WHAT_CHECK files in the > PDBREPORT databank for original PDB files or in the PDB_REDO databank for > their re-refined or rebuilt counterparts (note that PDB_REDO does not > explicitly do anything with ions, yet). > WHAT_CHECK uses the bond valence method to check for waters that should be > ions and ions that should be other ions or water and mines the > crystallisation conditions for hints of what could be there. > > HTH, > Robbie > > Sent from my Windows Phone > ------------------------------ > Van: Keller, Jacob > Verzonden: 6-3-2014 20:45 > Aan: [email protected] > Onderwerp: [ccp4bb] Validity of Ion Sites in PDB > > 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: [email protected] > ******************************************* > -- Jan Dohnalek, Ph.D Institute of Biotechnology Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 +420 226 201 571 Fax: +420 296 809 410
