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, 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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