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
