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
