Dear Dr. Philippe, There is no symmetry axis nearby the density. I did not computed anomalous map for this structure. In this structure, the occupancy of Co is only 0.4 (May be because I have added less Co). We have proved the presence of Co in one of our another crystal structure of same protein.
Thanks, Vijaykumar On 26 October 2017 at 23:11, Philippe BENAS < 00000d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all and Vijaykumar, > > I am personally much more concerned about the Co density which does not > seem as strong as expected for an atom with Z = 27, aren't you ? > > Also I was wondering if there is no symmetry axis around your unkown > density. Symmetry axes are often a garbage place for all the unexplained > density everywhere else in the a.u. > > Would you have by any chance computed an anomalous map ? It could help for > both your unknown density and the Co. > > Attached is a snapshot of 1.58 Angst. resolution structure showing a > 2mFo-DFc map in blue and contoured at 2 sigma level as well as an anomalous > map contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 > sigma. > > Best regards, > Philippe > > ------------------------------ > Philippe BENAS, Ph.D. > Dog in the manger > "Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui > glace le plaisir, - probablement comme un étranger tombant au milieu > d'enfants en train de danser une ronde", Alfred Delvau, Dictionnaire de > la langue verte (1866). > > Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS > Faculté de Pharmacie, Université Paris Descartes > Case 48 > <https://maps.google.com/?q=48+Av,+de+l'Observatoire&entry=gmail&source=g> > Av, de l'Observatoire > <https://maps.google.com/?q=48+Av,+de+l'Observatoire&entry=gmail&source=g> > F-75270 PARIS cedex 06 > +33.1.5373.1599 > E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr > URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , > http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 > ------------------------------ > > > > ------------------------------ > *De :* Nick Pearce <n.m.pea...@uu.nl> > *À :* CCP4BB@JISCMAIL.AC.UK > *Envoyé le :* Jeudi 26 octobre 2017 18h19 > *Objet :* Re: [ccp4bb] Unknown electron density > > I agree that the difference density isn’t “noise". However, just because > it’s not noise doesn’t mean that it is modellable (with an atomic model) — > the crystallographic density is an average over billions of molecules, and > if its not obvious at 1.6Å what is bound, then it’s probably a > superposition of states (or a highly disordered molecule with large > B-factors, which in this case amounts to pretty much the same thing). When > it’s a superposition of states in solvent regions, there are too many free > parameters to build a reliable model: you don’t know how many alternate > conformations to model, or how many species of molecules there are. It > could be 1 conformer of PEG with 1 superposed conformer of water or 2 of > PEG + 1 of water or 1 of PEG + 1 of something else + 1 of water… or > literally anything… > > So unless you have some prior information as to what is bound, I would > play it safe and model nothing — the conservative approach. > > Thanks, > Nick > > ————————————————— > > Nick (Nicholas) Pearce > Post-doctoral Researcher > Lab of Piet Gros > Crystal & Structural Chemistry Group > Universiteit Utrecht > > On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> > wrote: > > Thanks Nick. > > May be it is not that weak. The blue map contour level was set to 1.5. I > have attached another image in which the blue map is contoured to 1.0. I > feel the green density (contoured at 3.0) is not just some noise. > > On 26 October 2017 at 20:38, Nick Pearce <n.m.pea...@uu.nl> wrote: > > Hi, > > Given the weakness and shapelessness of the density I doubt it is "one > conformation of one thing", but rather a superposition of "one or more > conformations of one or more things”. If that is the case then there > probably isn’t enough information in the electron density or enough prior > information to restrain a modelling approach — i.e. you could build a model > that fit the density, but you could never determine if it was “correct”. I > would probably just leave that bit un-modelled. > > Thanks, > Nick > > ————————————————— > > Nick (Nicholas) Pearce > Post-doctoral Researcher > Lab of Piet Gros > Crystal & Structural Chemistry Group > Universiteit Utrecht > > On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> > wrote: > > Dear Dr. Vaheh, > > I tried fitting waters around Co but the positive density is still present > even after refinement. > > Thanks, > Vijaykumar > > On 26 October 2017 at 20:19, Oganesyan, Vaheh <oganesy...@medimmune.com> > wrote: > > Water molecules completing Co coordination? > > *Regards,* > > *Vaheh Oganesyan* > *www.medimmune.com <http://www.medimmune.com/>* > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Vijaykumar > Pillalamarri > *Sent:* Thursday, October 26, 2017 10:24 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Unknown electron density > > Dear ccp4bb, > > I am solving the structure of a 1.6 Angstrom data of a metallo protein. > While everything else is straight forward, this density (see the picture) > seems unfamiliar to me. I don't see any thing fits in the density. This > density present just above Histidine-Cobalt. What ever I try to fit, the > molecule clahes with histidine ( I mean the distance between His and > molecule is <2 Angstrom). > > The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% > glycerol. > > Any suggestions? > > Thanks, > Vijaykumar Pillalamarri > UGC-SRF > C/O: Dr. Anthony Addlagatta > Principal Scientist > CSIR-IICT, Tarnaka > Hyderabad, India-500007 > Mobile: +918886922975 > To the extent this electronic communication or any of its attachments > contain information that is not in the public domain, such information is > considered by MedImmune to be confidential and proprietary. This > communication is expected to be read and/or used only by the individual(s) > for whom it is intended. If you have received this electronic communication > in error, please reply to the sender advising of the error in transmission > and delete the original message and any accompanying documents from your > system immediately, without copying, reviewing or otherwise using them for > any purpose. Thank you for your cooperation. > > > > > -- > Vijaykumar Pillalamarri > UGC-SRF > C/O: Dr. Anthony Addlagatta > Principal Scientist > CSIR-IICT, Tarnaka > Hyderabad, India-500007 > Mobile: +918886922975 > > > > > > -- > Vijaykumar Pillalamarri > UGC-SRF > C/O: Dr. Anthony Addlagatta > Principal Scientist > CSIR-IICT, Tarnaka > Hyderabad, India-500007 > Mobile: +918886922975 > > > > > -- Vijaykumar Pillalamarri UGC-SRF C/O: Dr. Anthony Addlagatta Principal Scientist CSIR-IICT, Tarnaka Hyderabad, India-500007 Mobile: +918886922975
