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
>>
>> -------- Original Message --------
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>> Date: Wed, 30 Nov 2011 17:27:45 +0000
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>> To: Katia Baranova <[log in to unmask]>
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>>
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