Yes, I have. The cacodylate ion does not fit well into the density.On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan <[log in to unmask]> wrote:Did you try modelling in a cacodylate ion (CH3)2AsO2-?--On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu <[log in to unmask]> wrote:Paukstelis Research GroupBetty ChuDear 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/J5cKnO pCC4vb1VC
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,Department of Chemistry and BiochemistryUniversity of Maryland, College Park
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Pradeep Pallan