Re: [ccp4bb] Unknown positive electron density

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:

Re: [ccp4bb] Unknown positive electron density

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 f’’ for Ba at this wavelength is

Re: [ccp4bb] Unknown positive electron density

Betty, I think that f’’ 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 > wrote: Hi Craig, The

Re: [ccp4bb] Unknown positive electron density

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

Re: [ccp4bb] Unknown positive electron density

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 > wrote: Hi Shailesh, When I modelled in the Barium ion with octahedrally coordinated

Re: [ccp4bb] Unknown positive electron density

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

Re: [ccp4bb] Protein quantitaion based on extiction coefficient versus peptide bond

Hi, If you have the correct (experimentally-determined) extinction coefficients, the accuracy is usually very good. Often, however, people use calculated extinction coefficients, which can be off (usually not by more than 25%, so still OK for many purposes). One of the best practical ways to

Re: [ccp4bb] Unknown positive electron density

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

Re: [ccp4bb] Unknown positive electron density

Yes, I have. The cacodylate ion does not fit well into the density. On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan wrote: > Did you try modelling in a cacodylate ion (CH3)2AsO2-? > > On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu wrote: > >> Dear

Re: [ccp4bb] Unknown positive electron density

Did you try modelling in a cacodylate ion (CH3)2AsO2-? On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu 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 >

[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:

Re: [ccp4bb] BP3 error

Thank you for your quick reply. Crank2 seems to work very well when the job running. Thanks again. -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: ding...@iphy.ac.cn At 2017-08-21 15:02:53, "Navraj Pannu"

Re: [ccp4bb] BP3 error

Dear Wei, Thanks for reporting the error. Although it does not answer your question, I would strongly recommend to use crank2 over crank: it provides much better results. In fact, Pavol Skubak and I will probably shortly decide to only distribute crank2. I send this email with ccp4bb (cc'ed)

Re: [ccp4bb] Co-purified ligand present in protein crystal

Dear Wenhe, we had a similar case and extraction using CHCl3 plus CH3OH (2:1 ratio, v/v) (65 °C, 30 min) before mass spectrometry worked very well: https://www.ncbi.nlm.nih.gov/pubmed/21743455 Hope that helps, Tomas On Mon, Aug 21, 2017 at 4:41 AM, WENHE ZHONG

Re: [ccp4bb] Co-purified ligand present in protein crystal

Wenhe Potentially, mass spectrometry in combination with electron capture dissociation and/or collision-induced dissociation might be helpful. See doi: 10.1007/s13361-013-0662-5. Best wishes, Klaus === Dr. Klaus Fütterer

Re: [ccp4bb] Co-purified ligand present in protein crystal

Dear Wenhe, Are there other ligands known for this protein ? Could these be chemically modified and still interact with your protein ? Then you could use ligand affinity chromatography to purify your protein eluting with the same or other ligands. For me this the only way to obtain