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
