We had a similar case in our Eib structure (2xzr), with large peaks on a 3-fold. We initially thought it was noise, but Andrei Lupas convinced us to look more carefully, and it turned out to be chloride ion.
You could do an wavelength scan at a beamline looking for anomalous signal at the longest wavelength you can get to. If it's just noise, it shouldn't be particularly visible. If it is chloride or phosphate, you should at least have a peak there. Adrian On 1 Dec 2011, at 12:20, 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 >>>> >>>> -------- Original Message -------- >>>> Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK >>>> Date: Wed, 30 Nov 2011 17:27:45 +0000 >>>> From: JISCMAIL LISTSERV Server (16.0) <lists...@jiscmail.ac.uk> >>>> To: Katia Baranova <e...@mrc-mbu.cam.ac.uk> >>>> >>>> >>>> Listserv does not recognise you as a subscriber to the CCP4BB list using >>>> the >>>> >>>> e...@mrc-mbu.cam.ac.uk >>>> address so your message is unable to be distributed. You >>>> may be subscribed with a different email address and if you know what that >>>> is, >>>> re-send from there. >>>> >>>> If you still have problems, go to >>>> www.jiscmail.ac.uk/CCP4BB >>>> and subscribe to >>>> the list from the link Join or Leave CCP4BB >>>> >>>> or please contact the list owners at >>>> ccp4bb-requ...@jiscmail.ac.uk >>>> or >>>> >>>> helpl...@jiscmail.ac.uk >>>> >>>> >>>> >>> >>> >
