Looks like Ba2+. Since it exist with coordination number 6 or above check what geometry water is following there (trigonal bipiramidal or so on). Water might also be shared by symmetry related Ba cation.
Shailesh Kumar Tripathi, Phone: 9686289668 On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu <chube...@umd.edu> wrote: > Yes, I have. The cacodylate ion does not fit well into the density. > > On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan <pradeeppal...@gmail.com> > wrote: > >> Did you try modelling in a cacodylate ion (CH3)2AsO2-? >> >> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu <chube...@umd.edu> wrote: >> >>> Dear ccp4bb, >>> >>> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While >>> the model for the DNA fits very well into the density, there is a patch of >>> positive electron density in the solvent space that we are having trouble >>> with. >>> >>> The screenshot can be viewed through this link: >>> https://cbsostorage.chem.umd.edu/owncloud/index.php/s/J5cKnOpCC4vb1VC >>> >>> In the screenshot, the yellow color is the anomalous map and a barium >>> ion is fitted into density near the positive green electron density. >>> >>> The oligonucleotide was purchased from IDT. The crystallization >>> condition is 15% MPD, 120 mM BaCl2, and 30 mM NaCaC pH 6.4. I have tried >>> modelling Ba2+ with coordinated waters, MPD, and sodium cacodylate into the >>> electron density, but none of those fit well. >>> >>> Any suggestions regarding the identity of this electron density is much >>> appreciated. Thank you! >>> >>> Sincerely, >>> >>> Betty Chu >>> Paukstelis Research Group >>> Department of Chemistry and Biochemistry >>> University of Maryland, College Park >>> >> >> >> >> -- >> >> ------------------------------------------------------------------- >> Pradeep Pallan >> > >
