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 > <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
