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, ās 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
>>>
>>> -------- Original Message --------
>>> Subject: Rejected posting to [log in to unmask]
>>> 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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