Dear Vito,
I have also worked with iodinated and brominated compounds and in general the
light atoms are not flattened out. As John Helliwell pointed out, you may look
at series termination effects. However, since your map does not appear to be of
extremely high resolution, I guess all useful data will have been collected and
included.
The other thing to look at is occupancy. If your ligand is bound at partial
occupancy, the iodides will still have very strong density, but the lighter
atoms may fall below the 1 sigma threshold. You can test this by refining a
group occupancy for your ligand and also by scrolling down the contour level in
coot to see if some density appears at lower contour levels.
Good luck!
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Vito Calderone
Gesendet: Mittwoch, 10. Juni 2020 10:34
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Dear Pierre,
I was in particular talking of 2FoFc refinement maps.
In the attached picture for example you can see the 2FoFc map contoured at 1
sigma level of an I3C molecule bound to a protein where for I3C the only
visible density is that of iodines whereas the density of the other atoms of
the ligand is insignificant.
Best regards
Vito
-----Messaggio originale-----
Da: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Per conto di LEGRAND Pierre
Inviato: mercoledì 10 giugno 2020 09:31
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density
Dear Vito,
Could you precise in what kind of maps are you experiencing these effects:
2FoFc refinement maps or experimental phasing ?
I had this kind of effects long ago in experiemental phasing due to Fourier
transform ripple effects. This could be due to scaling problems, low resolution
truncation or incompletness (maybe intensity overloads).
Another source condition could be local X-ray dose degradation due to the high
absoption of the metals.
Best regards,
Pierre Legrand
PROXIMA-1, SOLEIL
________________________________________
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone
[calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom vs light atoms density
Dear All,
many of us have probably experienced that, in the diffraction of
protein ligands containing heavy atoms (cisPt, I3C, etc), the overwhelming
electron density of the metal can totally flatten that of the light atoms
around (or rather make it look insignificant).
Is anyone aware of an article/review (to use as a reference) in which this is
clearly stated/pointed out?
Best regards
Vito Calderone
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