Well - first thing to do is an DANO map and see if it is a metal ion.
The relative height of the DANO peaks for S and anything else can give
you some clues.
Eleanor
On 12/01/2011 10:20 AM, Carlos Kikuti wrote:
It's bang on the Y axis.... I'd just ignore it (treat it as just noise) and
work on the rest of the model. There seems to be some trouble in other parts of
it. (Had a similar case but at 3.5 A data). I wonder what is the gap between
Rfree and Rwork.
And I'm curious for what more experienced people will say about it.
Carlos
Em 01/12/2011, às 11:06, Mark J van Raaij escreveu:
although it is hard to see in 3 2D views, some of the tentacles appear
connected to the protein, could they result from some of the long Lys or Arg
side-chains not following the 4-fold symmetry? i.e. alternative conformations?
The density on the 4-fold may be ions, solvent, some metal ion? "Noise appears to
collect on symmetry axes" (for want of a better way to put it), so the sigma-levels
there are not very reliable. Sometimes one sees quite strong negative peaks on symmetry
axes that can not be explained, so I would expect spurious positive peaks to also occur.
Of course we normally just put a water in it if it can make reasonable hydrogen bonds.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
On 1 Dec 2011, at 10:36, Martin Montgomery wrote:
Posting on behalf of Katia Baranova (see below). Any suggestions gratefully
received!
Hello,
we have a puzzling density and hope someone has an idea of what it may be.
The pictures of it are here:
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/top.png
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/front.png
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/side.png
The space group is I422, resolution 1.6A
The trial contained Tris, DTT, EDTA, sodium, potassium, phosphate, and chloride.
The centre of our unknown feature is about 3.8A from the Arg and it is also on
the four fold symmetry axis.
It is + 28 sigma in the center and about + 9.5 sigma in each of the
"tentacles".
Thank you very much!
Katia.
On 30 Nov 2011, at 17:30, Katia Baranova wrote:
Hello,
Well, it doesn't work.
Can you forward it please?
thanks a lot,
K
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