Dear all and dear Jacob Please have also a look at another paper from Manfred where they show that "both difference electron-density maps and anomalous difference electron-density maps suggest that in crystals grown from a sodium sulfate solution PPE binds Na+ in its metal-binding site." [Porcine pancreatic elastase] : Weiss, M. S., Panjikar, S., Nowak, E. & Tucker, P. A. (2002). Acta crystallographica. Section D, Biological crystallography 58, 1407-1412
All the best, Philippe ________________________________ Philippe BENAS, Ph.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 ________________________________ ________________________________ De : Manfred S. Weiss <manfred.we...@helmholtz-berlin.de> À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Vendredi 7 mars 2014 13h02 Objet : Re: [ccp4bb] Validity of Ion Sites in PDB There is another paper out there, which describes the use of long wavelengths to define anomalously scattering substructures. This method certainly helps to distinguish water molecules from something else, such as chloride for instance. http://journals.iucr.org/d/issues/2007/03/00/dz5094/index.html Cheers, Manfred On 07.03.2014 11:12, Murray, James W wrote: > 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----- -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
