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 [email protected] >> Date: Wed, 30 Nov 2011 17:27:45 +0000 >> From: JISCMAIL LISTSERV Server (16.0) <[email protected]> >> To: Katia Baranova <[email protected]> >> >> >> Listserv does not recognise you as a subscriber to the CCP4BB list using >> the >> >> [email protected] >> 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 >> [email protected] >> or >> >> [email protected] >> >> >> > >
