Hi Betty, Could you post a few more screen shots of different orientations of the electron density?
If you see waters that are 1.6, 1.9 and 2.2 A away from the metal ion, I would try Mg2+ ion (trace amount of metal ions could be present in salt solutions/buffers as an impurity) and refine it (although 1.6Å is too close). In general, Mg2+ ions would show an octahedral geometry. On Tue, Aug 22, 2017 at 3:35 AM, <[email protected]> wrote: > Dear Betty, > > > > You have very high resolution, which helps you to identify your ligand, > but the ligand may be disordered… > > What I would do is to place some dummy atoms (e.g. waters) and refine and > look if the molecule gets clearer. By scrolling the density in coot, you > can identify the positions with the highest electron density were you > should put your dummy atoms. > > > > Looking at your pictures, as far as is possible without the ability to > rotate them, I would try to fit deoxyribose-phosphate, or even a complete > nucleotide. Maybe your prep contained some unreacted nucleotides and your > anomalous peak is phosphorus. > > > > Good luck! > > Herman > > > > *Von:* CCP4 bulletin board [mailto:[email protected]] *Im Auftrag von > *Betty Chu > *Gesendet:* Montag, 21. August 2017 17:19 > *An:* [email protected] > *Betreff:* [ccp4bb] Unknown positive electron density > > > > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__cbsostorage.chem.umd.edu_owncloud_index.php_s_J5cKnOpCC4vb1VC&d=DQMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oUauCRPJVt0_cKdOakQvtJoEkS4gY9JlJmXfkd2GnlI&s=0XTzg6Yyi4dgz7G80vogTkpLLMZoM8fj53buMeenlJM&e=> > > 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
