Dear Lumbini,
Thank you for sharing this picture.
Considering the low resolution and modest quality of your map, as
manifested in the "blobbiness" of the side chains near the green peak, the
"short distance" you mention is perhaps quite imprecise and thus not such a
barrier to tentatively placing a water molecule in that peak. What happens
if you do and re-refine?
Best wishes,
Gerard
--
On Wed, Sep 06, 2023 at 06:42:03PM +0530, Lumbini Yadav wrote:
> Dear Matthew,
> Below is the jpeg attached for the density at 4sigma.
>
> On Wed, Sep 6, 2023 at 6:21 PM Matthew Snee <matthew.sne...@manchester.ac.uk>
> wrote:
>
> > Is the density big enough for it to be phospho-tyrosine?
> >
> > Best wishes
> >
> > Matthew.
> > ------------------------------
> > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Lumbini
> > Yadav <lumbin...@gmail.com>
> > *Sent:* 06 September 2023 13:47
> > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
> > *Subject:* [ccp4bb] Density at a short distance near Tyrosine
> >
> > Hi all, I have determined the structure of a protein at 3Å resolution. The
> > protein has 6 chains in the asymmetric unit. In all these 6 chains I see a
> > density near tyrosine which is at a distance of 2. 1 from the OH group of
> > tyrosine. Since this
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> > Hi all,
> >
> > I have determined the structure of a protein at 3Å resolution. The
> > protein has 6 chains in the asymmetric unit. In all these 6 chains I see a
> > density near tyrosine which is at a distance of 2.1 from the OH group of
> > tyrosine. Since this distance is short for a hydrogen bond we are skeptical
> > about adding water molecules at this position. We have ruled out the
> > presence of a metal ion at that position.
> >
> > Any insight on what should be added in this density at this short distance
> > would be appreciated
> >
> > Thank you
> >
> >
> >
> > Regards
> >
> > Lumbini
> >
> > ------------------------------
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