Dear Vijaykumar, That looks great. So now what is the distance between the Co2+ and the unknown density blob ? Would it be compatible with a coordination bond of the Co2+ or not ?
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 Av, de l'Observatoire 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 : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> À : Philippe BENAS <philippe_be...@yahoo.fr> Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk> Envoyé le : Vendredi 27 octobre 2017 14h08 Objet : Re: [ccp4bb] Unknown electron density Dear Philippe, Here is the images showing anomalous map at Co contoured at 5. Thanks,Vijaykumar On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote: Hello Vijaykumar, Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't recognize the expected Co2+ coordination in your structure. I think evidence from an anomalous signal would be wellcome. Evidence from another crystal is not a proof for this crystal structure. It could be just a little stronger if the two crystals come from the same drop. You can get anomalous info even if the crystal was not collected at the wavelength that maximises f". For instance, the crystal for which I provided the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 Angst. is a common value for native data collection on synchrotrons so that I'm pretty sure you can get such signal from your data. And a good trick is to always process your data assuming the Friedel Law is not respected so that you can get quick access to the anomalous signal in case you need it. HTH,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 Av, de l'Observatoire F-75270 PARIS cedex 06 +33.1.5373.1599 E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- paris5.fr/spip.php?article18 De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Vendredi 27 octobre 2017 8h59 Objet : Re: [ccp4bb] Unknown electron density 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 Av, de l'Observatoire F-75270 PARIS cedex 06 +33.1.5373.1599 E-mails: philippe.benas@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) PearcePost-doctoral ResearcherLab of Piet GrosCrystal & Structural Chemistry GroupUniversiteit 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) PearcePost-doctoral ResearcherLab of Piet GrosCrystal & Structural Chemistry GroupUniversiteit 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 Oganesyanwww.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 PillalamarriUGC-SRFC/O: Dr. Anthony AddlagattaPrincipal ScientistCSIR-IICT, TarnakaHyderabad, India-500007Mobile: +918886922975To 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 -- Vijaykumar Pillalamarri UGC-SRF C/O: Dr. Anthony Addlagatta Principal Scientist CSIR-IICT, Tarnaka Hyderabad, India-500007 Mobile: +918886922975
