If you "multi-chicken" your 2fo-fc map in coot...
(Extensions > maps > multi-chicken)
... You might be able to pick out where different atoms are by comparing
the peak height with the near-by protein atoms (ADPs & occupancy
notwithstanding). At your resolution you will be able to see that O > N
According to your first fig. The Ser may carry a dual conformation. If
then, the occ ration could be ~ 7:3
According to your 1st, 2nd and 3rd figures, the geometry of the density is
tetrahedral. Can it be PO4 with the same occ (~70%) ?
If there were more figures available, the geometry of the
It is always worth doing a anomalous difference Fourier especially with
such high resolution data. Very easy if you are using CCP4 GUI2 - just ask
for it as part of your refinement run.
It is likely the high peaks could be S - but you can check by comparing
their height to that of a MET S peak .
Hard to see but maybe a transesterified serine like ser-o-AMP
Can you share the nature of the enzyme?
Artem
www.harkerbio.com
"Zoidberg was here"
On Feb 4, 2017 10:14 AM, "sharifah nur hidayah syed mazlan" <
shn.hida...@gmail.com> wrote:
> Dear All,
>
> I am working on a structure with an
That is some blob! What is the expectd ligand? It is hard to see in these
pictures but are there rings? other chemical features? to be seen
You could let Arp/War build dummy atoms into it - and see what it makes.
Eleanor
On 4 February 2017 at 15:03, sharifah nur hidayah syed mazlan <
I didn't see the figure, but I would not be surprised if cacodylate donates
a methyl group to make O-methylserine. Diethylene glycol is quite a bit
bigger than a methyl though.
Cacodylate is quite labile and undergoes radiolysis. It should probably
not be used for crystallization. If you
Dear John
A unit cell can be produced by the symmetry operations on an asymmetric
unit. So, in your summary, if you just include number of copies in the
asymmetric unit along with the space group, it should do the job.
On Sat, Feb 4, 2017 at 4:37 PM, <
Dear All,
Some papers write in the way that how many copies of proteins exist in the
crystal unit cell (for example, in each unit cell there was monomer or dimer or
3 proteins), some write in the way that how many copies of proteins exist in
the crystal assymetric unit.
I am writing a
