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 >
