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 > -- *************************** Jose Antonio Cuesta-Seijo Biophysical Chemistry Group Department of Chemistry University of Copenhagen Tlf: +45-35320261 Universitetsparken 5 DK-2100 Copenhagen, Denmark ***************************
