Priyank,
I think it's too far out from the Calpha to be Trp, and also not quite
flat enough. The map contains more information than just the shape as
to identity. Compare the max peak height of the 2Fo-Fc blob near the
Gln to neighboring element heights.
Much higher than C/N/O ? Probably not citrate, propanol etc
Much higher than S ? Probably not Cl, Mg, S, SO4, PO4
K is only a little heavier than S.
So you might cut down the range of possibilities considerably.
Partially occupied elements can be an issue, but you could narrow your
range of options. You can also do the expedient thing and drop an Au in
there with e.g. 0.5 occupancy (or a range of occupancies) and see what
the refinement does.
Phil Jeffrey
Princeton
On 12/10/13 7:44 AM, PriyankMaindola wrote:
dear members
i am trying to solve this crystal structure but
I am puzzled with an
undefined blob
that
appeared at a glutamine residue after refinement. I have attached pics
of that below.
Is it a covalent modification of acid-amide side chain..
... as there is no charged environment around and density seems continuous.
please suggest
....
following reagents were encountered by protein
during purification, crystallization and soaking
:
phenyl methyl sulfonyl fluoride
benzamidine
tris
dtt
(could it be cyclized dtt?)
k[au(cn)2]
acidic pH
isopropanol
citrate
sulfate
phosfate
K+, Na+, Cl-
map contour:
2fo-fc: 1rmsd
fo-fc (green): 3 rmsd
--
*Priyank*
