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 >>> >>> >>> >> >>
