Hello,
the guess about ripples is most likely correct. Just do this simple
experiment: place one iodine in a middle of a cubic box and compute
F-calc map. You will see aaaamazing picture! At least I enjoyed. You
will see a number of concentric shells of density around iodine,
positive and negative. Since in this numerical experiment there is no
any radiation damage, anomalous signals, local chemical environment and
things like that, so it is obvious that the effect can be attributed to
the Fourier series truncation ripples.
More nice pictures on this subject:
1) CCP4 Newsletter
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
2) Page 43:
http://phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1.pdf
3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16
Å Resolution: A.
Oliver Einsle, et al. Science, 1696 (2002) 297
4) Page 267 Figure 4:
On the possibility of the observation of valence electron density for
individual bonds in proteins in conventional difference maps
P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev
Acta Cryst. (2004). D60, 260-274
Pavel.
On 3/16/10 7:11 AM, Jose Antonio Cuesta Seijo wrote:
I am going to try to guess in this one.
As you say, the positions of the iodines cannot be challenged. But maybe
their occupancies can. Is there anomalous signal from iodine at your
wavelenght? Are you expecting radiation damage? In any case:
I see a spherical shell of low density around each one of the iodines. I
think this is a fourier ripple, at 1.x times the resolution for each atom
they seem to contribute negative electron density. Only that because the
iodines have so many electrons, this ripple can compete with the normal
possitive density of carbon atoms cancelling it out.
From the online protein crystallography course from Cambridge at
http://www-structmed.cimr.cam.ac.uk/Course/Convolution/convolution.html
"In addition, the Fourier transform of a sphere has ripples where it goes
negative and then positive again, so a map computed with truncated data
will also have Fourier ripples. These will be particularly strong around
regions of high density, such as heavy atoms."
Jose Antonio Cuesta-Seijo.
"Franck borel" <franck.bo...@ibs.fr> wrote:
Dear all,
We have a structure with triiodothyroninne (T3 hormone) in it. The
density around the ligand is very surprising.
According to the omit map the iodine atoms are not anymore directly
linked to the phenyl cycles (there is no more density between the iodine
and the carbon).
For one ligand an iodine seems now to be linked to the oxygen of the
hydroxyl group (image 2a), a second one seems to be attach to the cycle
through an "extra" atom (image 2b) and a third one seems to be too far
(2.2A) to be covalently bound to the cycle.
There is no reason for us to assume that such reactions may append. I
would like to know if this could be something real or if it is an
artefact due to the electronic properties of iodine, considering that
- the data are good to a resolution of 1.75 A
- the position of iodine atoms can not be challenged (I/sigma >20)
Thanks for your help
Franck BOREL
INSTITUT DE BIOLOGIE STRUCTURALE Jean-Pierre Ebel
UMR5075 CEA-CNRS-Univ. J. Fourier
LCCP / Groupe Synchrotron
41, rue Jules Horowitz
F-38027 Grenoble Cedex 1 - France
Phone:33 (0)4 38 78 59 05
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Jose Antonio Cuesta-Seijo
Biophysical
Chemistry Group
Department of Chemistry
University of Copenhagen
Tlf:
+45-35320261
Universitetsparken 5
DK-2100 Copenhagen,
Denmark
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