Well I would start by flipping the carbonyl oxygen then see if the side chain can use the density - what are the B values for the neighbouring stuff? Eleanor
On 25 October 2013 19:00, Patel, Joe <joe.pa...@astrazeneca.com> wrote: > Is that a glycine in the sequence next to the Glu/Gln? Have you tried > building a 50% occ of the backbone in that region in two conformations, and > then a water molecule further up into the feature. The density over the > carbonyl looks weak and you have some negative density there that might > indicate mixed conformation. > > Just an idea, hard to tell from still images if my idea would work. > > Joe P > > > -------------------------------------------------------------------------- > Confidentiality Notice: This message is private and may contain confidential > and proprietary information. If you have received this message in error, > please notify us and remove it from your system and note that you must not > copy, distribute or take any action in reliance on it. Any unauthorized use > or disclosure of the contents of this message is not permitted and may be > unlawful. > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jose > Artur Brito > Sent: Friday, October 25, 2013 1:29 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Unusual electron density - any guesses?? > > Dear All, > I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. > The model is pretty much finished but I see a strange electron density that I > can't imagine what it is. > > Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ > . Any pointers/guesses are most welcome. > > In short, I see an oblong piece of density coming straight out of the > main-chain!! It doesn't refine as a "chain" of waters and any small piece of > PEG doesn't refine properly either (actually, not sure if this would make any > sense but since the crystallization condition is PEG3350 and gave it a try!!). > > The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. > The protein was purified from recombinant expression in E. coli with > "trivial" reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... > > Wishing you all an excellent weekend, best regards, Jose > > > -- > ************************************************ > * José Artur Brito, PhD * > * * > * Post-Doctoral Fellow * > * Membrane Protein Crystallography Lab * > * Instituto de Tecnologia Química e Biológica * > * Oeiras - Portugal * > * * > * Tel.: +351.21.446.97.61 * > * Fax: +351.21.443.36.44 * > * * > * E-mail: jbr...@itqb.unl.pt * > * URL: http://mx.itqb.unl.pt * > ************************************************
