Colleagues-
We regret to announce the untimely death of Dr. Chris Dealwis, Associate
Professor of Pharmacology at Case Western Reserve University (CWRU), in
Cleveland, Ohio. Chris worked on several important macromolecular
structures, including renin, chemokines, amyloid-recognizing antibodies,
inquiries to Dr. Chris Pursell, chair of the search committee
and the department, at chris.purs...@samford.edu.
Thank you-
Brad Bennett, Ph.D.
Search Committee Member
Assistant Professor of Biology
Samford University
bbenn...@samford.edu
205-726-4523
Hi all-
I am trying to merge 3 Scalepack .sca files into 1 MTZ file using Aimless
in CCP4i (CCP4 version 6.4.0). However, Aimless fails with the error that
it does not recognize my rhombohedral space group (R32).
#CCP4I TERMINATION STATUS 0 Spgr_descr: No such HM symbol
I'm used to this as in
Yes, but the technique is still in its infancy stage.
DOI: 10.1016/j.sbi.2014.03.004
Cheers-
Brad
On Fri, Aug 29, 2014 at 6:34 AM, rana ibd
0285de88044a-dmarc-requ...@jiscmail.ac.uk wrote:
Dear CCP4
I wanted to ask has anyone tested 3D protein structure by cryo-electron
microscopy?
, but those are
slowly falling.
Some reading material
http://www.ncbi.nlm.nih.gov/pubmed/23181775
http://www.ncbi.nlm.nih.gov/pubmed/25071206
Cheers
Marcus
Quoting Brad Bennett bradbennet...@gmail.com:
Yes, but the technique is still in its infancy stage.
DOI: 10.1016/j.sbi
Hi Raji-
To echo what John Lee said, we found that we had to maintain a ratio
between 1:2 and 1:10 Ulp1:substrate for several different target proteins,
none of which were membrane proteins however. So, I would definitely try
maybe a 1:5 ratio and see what happens. This wasn't too cost prohibitive
Thanks to Jon, Huw, and Albert for quickly setting my mind at ease about
upgrading our Mac OS to Mountain Lion and compatibility with CCP4. Just as
an FYI, it seems most of the other commonly used software packages (i.e.
Phenix v1.8, PyMol v1.5) are ok running on 10.8 as well.
Best-
Brad
On Fri,
Hi all-
Sorry if this has been gone over before but I could not find a direct answer
after a cursory search in the archives and online. Is the CCP4 suite compatible
with Mountain Lion? Specifically, the GUI (ccp4i) and Coot? Our Macs are
running Leopard and Snow Leopard and we've been thinking
Hi all-
I have 2 PDB files of the same protein (in slightly different states) and I
want to output a table of interactions (preferably hydrogen bonds, salt
bridges) that are unique to a structure i.e. Ser22 OG forms a hydrogen bond to
Lys25 NZ in structure 1 but not in structure 2. In other
I think it was an N-terminal RGS-type His tag in 3O8Y (human lipoxygenase)
that mediated crystal contacts with a symmetry related molecule. As I
recall, this tag composed a B-strand that formed a nice interface with a
native B-strand of the symmetry related molecule. Pretty cool...
-Brad
On Wed,
I'll just second, third, and fourth the assessment of the Qiagen
anti-pentaHis antibody. I pretty much gave up on anti-His antibodies until
we tried this out in the lab and now everyone loves it. Reasonable
sensitivity and specificity (we use IR dye-conjugated secondaries and a
Li-Cor Odyssey
Native PAGE (i.e. BN-PAGE), light scattering (i.e. MALLS)
Not quick and easy but could work: AUC (i.e. a sedimentation equilibrium
experiment)
-Brad
On Tue, Jun 26, 2012 at 9:01 AM, Careina Edgooms
careinaedgo...@yahoo.comwrote:
Dear ccp4 bulletin board
I apologise for off topic question. I
Hello Dr. Palmer-
There may be other representatives in the literature by now but the one
study I know of that examines the usefulness and limitations of determining
cryo-neutron structures is The 15-K neutron structure of saccharide-free
concanavalin A, Blakeley et al. (2004), PNAS,
Is it ok for you to heat your sample? If so, you could near-boil your
sample in a heating block, say at 95 degrees C, in order to concentrate
it. I've done this in regular 1.5 mL eppendorf tubes with either the cap
open or where I've punctured the top of the cap with a narrow bore needle
(in order
Hi SnowDeer-
What's your precipitant? Have you tried lowering that as much as possible?
This will likely delay nucleation and crystal growth but the crystals will
also likely be larger (and perhaps more well ordered). Of course, you may
reach a lower limit where you prohibit nucleation. You'll
Though I'm not meaning to turn this into a plaque assay burn session, for
many reasons we have also abandoned it and instead titer our baculovirus
stocks (P3 and P4) using flow cytometry. We use an antibody against viral
gp64 that has been labeled with PE and stain infected cells in 96 well
plates
Hi Harry-
X-ray crystallography played an integral part in discoveries made in Michael
Crichton's Andromeda Strain. Mainly it was used to determine the elemental
composition and arrangement of the capsid or shell that the foreign
organism was found within.
Best-
Brad
On Thu, Apr 15, 2010 at
Hi Amit-
We used a well-expressing soluble protein fusion (SUMO) at the N-term of a
couple of B. anthracis proteins that we were trying to produce in E. coli,
which improved the soluble yield of both targets tremendously. The
disadvantage of a fusion is of course you produce a non-native protein-
Hi Ajit-
Sounds like maybe you haven't defined the refinement to include your waters
explicitly. Did you edit the parameter list near the top of the .ins file
(like ISOR, CONN, BLOC commands) to include your newly added waters?
HTH-
Brad
On Fri, Feb 12, 2010 at 4:45 PM, Ajit Datta
Hi Fengxia-
How about increasing the PEG% so you don't have to add as much other
cryoprotectant?
Also, have you tried annealing the crystals? I've had success with this when
I've had samples diffract similarly. The simplest way is by blocking the
cryostream for 2-3 seconds (repeat 1-2 times) and
Wow, the CCP4BB has proved once again its awesome community spirit. Thanks
to all who replied so promptly for my request for graphics showing density
improvement (and more accurate modeling) with an increase in data
resolution. Below is a summary of the responses:
Several people pointed to James
Hi all-
I recall seeing a long time ago a figure which showed the progressive
improvement of electron density as one increases resolution, say from 6 to
3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
the ability to model side chains of alpha helices at higher
James-
It's:
lnKd = deltaH- RT(deltaS)
As for Km ~ Kd, here be dragons...Km values cannot be treated as the Kd of a
complex because dissociation of a catalytic complex has two potential fates,
one that is denoted by a rate constant that is correlated to turnover (so,
the forward reaction leading
Hi Dan-
There's an online server and program called DPX which will calculate the
depth of all the atoms in your PDB file. An atom's depth is defined as the
minimum distance it is to the nearest solvent accessible atom, with depth =
0 meaning the atom is not buried at all (most likely at the
Hi Ivan-
Since you most likely have the data to back it up and I assume you have the
computational firepower to do it, why don't you run a full matrix refinement
in SHELX to get estimates of bond lengths and their deviations? It's worked
for me in calculating carboxylate C=O bond lengths to
Hi Atlanta-
Yep, this one bit me (on Mac OS X), too. To fix it, I had to go to
/usr/local/ccp4-6.1.2/share/ccp4i/etc/UNIX and edit my configure.def file.
Almost at the end of the file, there is a line that says
USE_DBCCP4I_ON_STARTUP. Change the value from 1 to 0. This should
refresh your project
install (as does xloggraph
and xccpjiffy2idraw).
On Wed, Aug 12, 2009 at 10:49 AM, Brad Bennett bradbennet...@gmail.comwrote:
Hi all-
CCP4 distribution: 6.1.1
OS: Mac OS X, version 10.5.7 (Intel)
I wanted to look at a plot output (.plt file) from a POLARRFN run invoked
within ccp4i. When
Hi Riya-
Expression Systems has a protocol for SeMet incorporation (Click on the
Selenomethionine Incorporation pdf file at
http://www.expressionsystems.com/?mvcTask=documents) and they advertise that
they do just about anything you would want to do with insect cells (see
Hi all-
CCP4 distribution: 6.1.1
OS: Mac OS X, version 10.5.7 (Intel)
I wanted to look at a plot output (.plt file) from a POLARRFN run invoked
within ccp4i. When attempting to open the plot file, I get a Bad plot84
file format but the archaic xplot84 driver window does open just with no
plot
Hi all-
Got a perplexing thiol chemistry/phasing issue. To prevent non-native
disulfide bonds from forming between free Cys but to preserve native
disulfides, I have heard of using a very low (say 0.5 mM) concentration of
DTT. I've recently come across a paper where the assignment of 3 disulfides
Hi Kien-
Are you basing extensive proteolysis (degradation) on an SDS-PAGE result
alone? Are you monitoring the elution profile from Ni/NTA? Do you see
numerous A280 peaks for your elution? Sample prep of membrane proteins for
SDS-PAGE is very trial-and-error. Heating the samples may cause weird
Hi Raji-
A number of GPCRs have been overexpressed in E. coli. Examples are Reinhard
Grishammer's work with neurotensin receptor and Christopher Tate's work with
B2-adrenergic and adenosine 2a receptors. The problem was not necessarily
expression but proper outer membrane targeting of *active*
Like most things (and scientists in general I suppose), SUMO tags have both
a good and a naughty side. Like GST, in my hands, they enhanced expression
and solubility of a couple of different target proteins. Their primary
advantage is that when you clip off SUMO with the SUMO protease (aka Ulp1)
FWIW, many of the crystals used in classical neutron diffraction
experiments were pretty elderly samples by the time data collection was
initiated, partly to allow large crystals to grow ever larger, partly
because of the mandatory deuterium exchange process and partly because the
experiments
Hey Yong...
add 10 mM ATP + 2.5 mM MgCl2 in your purification buffer and wash it off during
your affinity step...this has worked for me (of course make sure that you're
not unlucky and your protein doesn't elute during this step; don't worry it
shouldn't)
if that doesn't work, maybe try
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