Dear Vito,
In that case, and from what I can see from the picture you shared, I would
guess that it is mainly the effect of the low occupancy of this I3C. The peak
height of the iodide atoms seems low.
Pierre
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito Calderone
[calder...@cerm.unifi.it]
Envoyé : mercredi 10 juin 2020 10:54
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density
Dear John,
I would say that in that case the FoFc is basically flat.
Vito
Da: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Per conto di John R Helliwell
Inviato: mercoledì 10 giugno 2020 10:40
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density
Dear Vito,
The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
It maybe is more akin to the situation we described here:-
https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
ie what does your Fo-Fc map, with three iodines placed, at the correct
occupancy, look like?
Best wishes,
John
Emeritus Professor John R Helliwell DSc
On 10 Jun 2020, at 09:34, Vito Calderone
<calder...@cerm.unifi.it<mailto:calder...@cerm.unifi.it>> wrote:
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<mailto:CCP4BB@JISCMAIL.AC.UK>>
Per conto di LEGRAND Pierre
Inviato: mercoledì 10 giugno 2020 09:31
A: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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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