[ccp4bb] Phosphorylated arginine in COOT

2019-07-26 Thread Anirudha Dutta
Hello everyone
>From electron density, It looks like one of the arginines in my protein is
post-translationally modified as phospho-arginine. How to make sure it's a
real phospho-arginine, not an arginine interacting with phosphate or
acetate ion? The resolution of the structure is 2.3 A. Can anybody helps me
with step by step procedure to incorporate a phospho-arginine in my
structure using COOT and if anything special need to be done during
refinement in Phenix.
Thanks and regards
Sincerely
Anirudha Dutta



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Re: [ccp4bb] Resonant Scattering Directionality

2019-07-26 Thread Tim Gruene
Dear Jacob,

closely related to Ethan's explanation, but not quite the same, the 
contribution of f' and f" is still affected by the fall off from the ADPs, i.e. 
they also fall off exponentially, even for high quality crystals with a very 
low B-factors.

The effect that you describe, however, still has to be accounted for during 
refinement, which is why you have the DISP command in SHELXL.

Best,
Tim

On Thursday, July 25, 2019 8:23:34 PM CEST Keller, Jacob wrote:
> Dear Crystallographers,
> 
> It seems to be a usual assumption that anomalous scattering is essentially
> angularly-independent, e.g.:
> 
> http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm
> 
> But why the can't we see anomalous-only spots at e.g. 1 Ang resolution in a
> 2 Ang data set?
> 
> This actually has some repercussions for a non-x-ray (but still resonance)
> idea, so it would be helpful to know...
> 
> All the best,
> 
> Jacob
> 
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
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Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

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