Fourier truncation ripples? JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CRAIG A BINGMAN Sent: Monday, August 21, 2017 6:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Unknown positive electron density Betty, I think that fââ for Ba at this wavelength is around 3.5 electrons, and f'' for As is expected to be about 3 electrons. Is there a nearby crystallographic symmetry axis? Craig On Aug 21, 2017, at 5:05 PM, Betty Chu <chube...@umd.edu<mailto:chube...@umd.edu>> wrote: Hi Craig, The data collection wavelength was 0.92 Angstroms. Since we observe anomalous signal for Ba at this wavelength, we would expect greater anomalous signal if As were present. There is a possibility for weak anomalous signal in this positive density, but the weak anomalous signal only shows up if I try to model a Ba in the density. Without modelling anything, there is no anomalous signal. This is what the map looks like after one round of refinement with the Ba in the density. But since there are waters that are 1.6 Angstroms, 1.9 Angstroms, and 2.2 Angstroms away from the Ba, which is smaller than the coordination distance between Ba and water, we are skeptical of the Ba being there. https://cbsostorage.chem.umd.edu/owncloud/index.php/s/O4lI2iKvRsQUoRo Thank you, Betty On Mon, Aug 21, 2017 at 5:21 PM, CRAIG A BINGMAN <cabing...@wisc.edu<mailto:cabing...@wisc.edu>> wrote: What is the data collection wavelength/energy? Would you expect significant anomalous diffraction from As at this wavelength? On Aug 21, 2017, at 11:37 AM, Betty Chu <chube...@umd.edu<mailto:chube...@umd.edu>> wrote: Hi Shailesh, When I modelled in the Barium ion with octahedrally coordinated waters and ran the refinement, the distances from the barium to some of the waters ended up being too close (<2.2 Angstroms). Also, the positive electron density is connected. If the density indicated barium with coordinated waters, would that mean there are multiple ones present in the positive density? Here are more views of the connected positive density. https://cbsostorage.chem.umd.edu/owncloud/index.php/s/j5CgZIJe6NKgUlZ https://cbsostorage.chem.umd.edu/owncloud/index.php/s/YbiNFbT8AW1iHUQ On Mon, Aug 21, 2017 at 12:00 PM, Shailesh Tripathi <shailes...@gmail.com<mailto:shailes...@gmail.com>> wrote: Looks like Ba2+. Since it exist with coordination number 6 or above check what geometry water is following there (trigonal bipiramidal or so on). Water might also be shared by symmetry related Ba cation. Shailesh Kumar Tripathi, Phone: 9686289668 On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu <chube...@umd.edu<mailto:chube...@umd.edu>> wrote: 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<mailto: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<mailto: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
