Dear all, It is well known that you can look at anomalous difference maps to see heavier atoms - although I think not enough people do it. One technique that I think is powerful, but under-used is to calculate element-specific maps by taking the difference of anomalous difference data from just above and below the absorption edge. This paper introduces the technique and explains it well http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html. I suspect if this method were more used, many mis-labeled metals in proteins would come to light.
James -- Dr. James W. Murray Lecturer in Biotechnology Dept. Life Sciences Imperial College, London Tel: +44 (0)20 759 48895 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Friday, March 07, 2014 9:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Validity of Ion Sites in PDB -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Jacob, the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/ lists a couple of references which might be of interest. As usual in crytallography one must understand the science in order to understand the reliability of the models from the PDB. They are not the truth but only models to explain the data from a diffraction experiment. Best, Tim On 03/06/2014 08:45 PM, Keller, Jacob 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 > ******************************************* > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTGZUEUxlJ7aRr7hoRAtC+AKDr6cJzgWgUAWPO6AYmDHMlFs6gbwCg8+E/ Yj2NVdKiYBq9O28v9eCQWDA= =YkXc -----END PGP SIGNATURE-----
