Ionic Ba2+ has smaller radius 2/3 of metalic Ba. So it will have increased e/A3 and modelling Ba atom might give positive density centered at Ba site. This discussion might help:
http://ccp4bb.blogspot.in/2011/11/atomic-scattering-factors-in-refmac.html Shailesh Kumar Tripathi, Phone: 9686289668 On Tue, Aug 22, 2017 at 5:32 AM, Keller, Jacob <kell...@janelia.hhmi.org> wrote: > 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> 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> > 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> 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> > 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> 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> > 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> 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 > > > > > > > > > > > > >
