Hi Shailesh, When I modelled in the Barium ion with octahedrally coordinated waters and ran the refinement, the distances from the barium to some of the waters ended up being too close (<2.2 Angstroms). Also, the positive electron density is connected. If the density indicated barium with coordinated waters, would that mean there are multiple ones present in the positive density?
Here are more views of the connected positive density. https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi <shailes...@gmail.com> wrote: > 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 >>> >> >> >
