Thank you all for your replies and suggestions. I have fitted in some dummy waters as Herman suggested and this is the result after one round of refinement. The waters are positioned where there is highest electron density, but I am not sure how to move forward from here.
https://cbsostorage.chem.umd.edu/owncloud/index.php/s/VTQ6Uinp1UVIWGR https://cbsostorage.chem.umd.edu/owncloud/index.php/s/NUZKClayzSMn7PP https://cbsostorage.chem.umd.edu/owncloud/index.php/s/0FZhxtgcQhhqnaA I have also tried fitting in a nucleotide, but the geometry of it does not fit the density well. We do not think this is due to Fourier truncation ripples since the positive density is not at the crystallographic symmetry axis. Betty On Tue, Aug 22, 2017 at 10:34 AM, Pradeep Pallan <pradeeppal...@gmail.com> wrote: > 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, <herman.schreu...@sanofi.com> 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:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag >> von *Betty Chu >> *Gesendet:* Montag, 21. August 2017 17:19 >> *An:* CCP4BB@JISCMAIL.AC.UK >> *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 >
