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Dear Vito
I looked at the examples of I3C in 3e3d, 3e3s and 3e3t and certainly the latter
two show clear 2Fo-Fc for several I3Cs at a range of occupancies. So my mention
of the different difference maps’ effectiveness does not apply.
Hermann and Eleanor suggestions hopefully will explain your
Hmm - of course heavy atoms will affect the sigma level of a map, but that
is easily adjusted - just scroll till the electron density looks sensible
for some well defined protein atoms. (Ideally I guess we should contour at
some absolute density level but choosing that to take account of
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
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
Dear John,
I would say that in that case the FoFc is basically flat.
Vito
Da: CCP4 bulletin board 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
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?
Dear Vito,
We accumulated quite a good deal of knowledge of this type of complex, firstly
the platins, then later, led by Dr Alice Brink, rhenium complexes with
proteins. This review describes some of this:-
https://pubs.rsc.org/en/content/articlelanding/2017/mt/c7mt00219j#!divAbstract
The
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
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
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