I am even more cautious - if I want to check the anomalous map for a strong scatterer I set the putative anomalous scatterer occupancy to 0.0 . Theoretically it shouldn't be necessary - the atom map uses Phic+90 (or maybe Phic -90??) but if the site is excluded you feel more secure in drawing conclusions.
Eleanor On 25 August 2017 at 20:31, James Holton <[email protected]> wrote: > That just looks like bulk solvent to me. Might be extra dense to the the > barium, but disordered bulk nonetheless. > > If, as you say, the anomalous peak only shows up after you model in a > strong anomalous scatterrer and not when you don't model in anomalous > signal, then I suspect all you are seeing is the fabled "model bias". Weak > signals (like anomalous) are particularly sensitive to this. > > It is an interesting test to try: > 1) measure the anomalous difference peak height after refinement (I use > "peakmax" in CCP4) > 2) set the Ba atom's f" value to 0, and re-refine to convergence. What is > the peak value now? > 3) set the Ba atom's f" value to twice what you expect theoretically. > Re-refine. Now what do you see? > > Once you've done this, you should have a good feeling for how much of your > anomalous peak is coming from your model vs from your data. > > -James Holton > MAD Scientist > > > On 8/21/2017 3:05 PM, Betty Chu 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 <[email protected]> > 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 <[email protected]> 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 <[email protected] >> > 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 <[email protected]> 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 < >>>> [email protected]> wrote: >>>> >>>>> Did you try modelling in a cacodylate ion (CH3)2AsO2-? >>>>> >>>>> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu <[email protected]> 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 >>>>> >>>> >>>> >>> >> >> > >
