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:
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
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
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
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
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
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
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
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
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
>
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:
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"
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)
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
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
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
16 matches
Mail list logo