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 > <mailto: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 >> <mailto: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 >> <mailto: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 >> <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Vijaykumar Pillalamarri >> Sent: Thursday, October 26, 2017 10:24 AM >> To: CCP4BB@JISCMAIL.AC.UK <mailto: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
