Dear All,
Thank you Folmer and Fred for your suggestions. Mine is
an isomorphous crystal. I had refined without using the
same set of Rfree reflections, finally getting larger
difference between the R and Rfree. I hope considering
the same Rfree set would solve this problem.
Thank you
With
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Dear Kavya,
As far as I understand the PDBRedo project attempts to make the
reflections unbiased from the structure by a random shift of
coordinates (e.g. 'NOISE' keyword in pdbset, although I am not aware
of an investigation about whether this
Dear all,
the recent advertisement for a postdoc position in the Freemont/Zhang
labs at Imperial had a small error in the job code needed to find it
online. The correct code is
NS 2013 047 IL
Use it at http://www3.imperial.ac.uk/employment (Job search) to apply
for the position. Closing
Hi Ed,
It looks as though you have not sourced $CCP4/include/ccp4.setup.
This needs to be customized and sourced before you configure and make
CCP4.
Adam
Hi Tim,
Our approach is a bit different. We first try to establish whether the
R-free set is biased, by checking whether R-free is surprisingly low
compared to R given the data parameter ratio. If this is the case (or if we
chose a new R-free set for some reason, e.g. because it was too small)
Along these lines, what reagents do people use to promote disuflide bonds,
i.e., the anti-DTT?
JPK
On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote:
You might want to try Disulfide by design
http://cptweb.cpt.wayne.edu/DbD2/
Cheers
Dave
On Feb 28, 2013 6:55
Rather than looking at anti-DTT it is more important to set up an
appropriate redox system. This can be a combination of reduced and
oxidised glutathione or cysteine. If you check some of the commercial
protein refolding screens this should give you an idea about relative
concentrations.
Best
Dear Colleagues,
We are offering an exciting PhD studentship on the structural biology of RNA
degradation and translational repression. The project combines state-of-the-art
technologies in cryo-electron microscopy and X-ray crystallography and is a
collaboration between the Spanish
Along these lines, what reagents do people use to promote disuflide bonds,
i.e., the anti-DTT?
Glutathione (red) + Glutathione (ox), redox potential is adjusted by
varying the ratio.
Best,
Clemens
JPK
On Thu, Feb 28, 2013 at 2:06 AM, David Briggs
drdavidcbri...@gmail.comwrote:
You
We have had some good luck with hydrogen peroxide [for technical details plus
validation via a crystal structure see Van der Meeren et al JBC
288(2):1214-1225, (2013)].
best of luck
Savvas
On 28 Feb 2013, at 12:14, McEwan, Paul paul.mce...@evotec.com wrote:
Rather than looking at
Adam,
I am not compiling CCP4, just refmac. IIUC, all that sourcing
ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c
and libccp4f. And presumably lapack and libblas, but that's a separate
issue.
On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote:
Hi Ed,
It looks
In the literature, you can find examples of air oxidation, oxidized
glutathione (alone), mixture of reduced and oxidized glutathione, and
hydrogen peroxide. The correct concentrations have to be found
empirically. We are just now mushing through this with an engineered
disulfide variant. Air
Dera Careina
going back to the original software question, I think you may be able to use
the Rasmot-3D Pro server
http://biodev.cea.fr/rasmot3d/
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W459-64. doi:
10.1093/nar/gkp304. Epub 2009 May 5.
RASMOT-3D PRO: a 3D motif search webserver.
I don't know how much mileage you'd get out of it with your protein, but
I was able to get very efficient disulfide linkage at the dimerization
interface of my protein by dropping the salt to nearly nothing and
running lots of buffer over it after immobilization on a cation exchange
column
Adding 1-10mM copper sulfate is often a good way to oxidize disulfide bonds,
although some proteins cannot tolerate this treatment.
Mike
- Original Message -
From: Jacob Keller j-kell...@fsm.northwestern.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, February 28, 2013 3:09:18 AM GMT
I have used a copper solution that worked well. The details can be found in
this paper: Nucleic Acids Res. 2004 Sep 30;32(17):5192-7. PMID: 15459288 PMCID:
PMC521666
Yingyun Liu
- Original Message -
From: Roger Rowlett rrowl...@colgate.edu
Date: Thursday, February 28, 2013 9:52 am
Dear Colleagues,
We have an Industrial CASE BBSRC PhD Studentship on offer at the University
of Reading. Please circulate this email to relevant colleagues and UG
students.
The CASE award is a collaborative project in the Schools of Food and
Nutritional Sciences and Biological Sciences. The
Hi All,
I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) with 2GB
nVIDIA Quadro 4000. Can anyone recommend to me which stereo monitor would
be compatible with this model?
I have some stereo models mentioned in previously ccp4bb email:
- Zalman ZM-M215W 21.5in
- Zalman
All,
The West Coast Protein Crystallography Workshop is fast approaching. We have a
pretty full house with an outstanding line up of talks and posters! If you
would still like to participate we can accommodate more people (see wcpcw.org).
That said, we absolutely need your abstract first
Thank you to everyone for the helpful suggestions
From: Yingyun Liu yingyun...@jhu.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, February 28, 2013 10:29 PM
Subject: Re: [ccp4bb] disulfide engineering
I have used a copper solution that worked well. The details
What about the ASUS VG278HR
Activ stereo with build in emitter, 27 in.
Am 01.03.13 00:56, schrieb jlliu liu:
Hi All,
I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) with 2GB
nVIDIA Quadro 4000. Can anyone recommend to me which stereo monitor would be
compatible with this
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