POST-DOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY, THE UNIVERSITY OF
QUEENSLAND, BRISBANE, AUSTRALIA
Applications are invited for a protein crystallography post-doctoral
position in the laboratory of Prof Bostjan Kobe at the School of Molecular
and Microbial Sciences (SMMS) and the Institute for
Hi again,
Thank you for your reply.
I know that the loop regions are notorious for crystallization however in this
case it is yielding the crystals but with lower quality. Does it not due to the
quick crystallization, the lattice has no time to form up. Thats why it is
happening.
Can I n
...forgot to mention
I used Q sepherose from Sigma for the IEC
Dear bbers,
Sorry to post a job here...
One postdoctoral position is available immediately at the Center for
Membrane Biology, Department of Biochemistry and Molecular Biology, The
University of Texas Health Science Center at Houston.
(http://www.uth.tmc.edu/cmb/) The successful candidate w
Hi there,
I have trouble with normal glycerol cryoprotectant. My protein crystals seems
not stable in it. However, my mother liquor has extremely high concertration of
Nonyl-maltoside (estimated ~20%, this membrane protein really needs that high
detergent, sounds weird.8)So, I am wondering
Hello everyone,
I am working on a yeast membrane protein, about 100 KDa.
The protein is expressed as an inclusion body in E coli even at 18 C. The
problem is solved when MBP is fused to the N terminus of the protein.
The resulting protein is ~140 KDa, pI 6.0. The expression level is moderate.
Afte
Hello everyone,
I have a question about ion exchange chromatography.
- I have a membrane protein (pI 9.5), 13 KDa
- It's fused to MBP (maltose binding protein pI 5.1, 44 KDa) to prevent
inclusion body formation during high level expresscion.
- The final protein has a pI of 6.1, 57 KDa
--> The p
Hello,
I have attached a log file from a refmac refinement output that was initiated
by ARPwARP (the flexwarp program in CCP4) after an initial model building was
determined good. This is the refmac model refinement when the ARPwARP program
starts a separate job to refine or finalize the mode
Dear all,
I may sound stupid enough.
I tried the PMS-DCPIP assay system as suggested, and I choose to observe the
absorption at 600nM. However, when I initialize the reaction, I actually see
the Abs slowly but steadily increasing rather than decreasing.
How the FAD interact with the enzyme is
We have an Ocean Optics USB-4000 unit in our lab. It does everything
from quantifying protein and nucleic acids, spectrophotometric
titrations, and metalloenzyme spectra at low volume/concentration. It's
not a toy, but a diode array spectrophotometer that has excellent S/N
and resolution. You c
CCP4 bulletin board wrote on 12/04/2008 02:50:30
PM:
> Thank you all for suggestions and explanations. I did not make it clear.
The
> tilt angle I wanted to restrain is the one from a C-OH bond to a plane
> (The C is in the plane). The O atom of OH group is not in the planar
> restraint in the ci
I want to add I absotely hate the nanodrop. We've had a demo for it, and
found the readouts to be very unreliable. Fluctuations of 20% and more.
Just leaving the same drop in and measuring the sample multiple times gives
different values (going in both directions, so not only due to
evaportations
Hi Huiyang
OK sorry for misunderstanding. I think that kind of out-of-plane
restraint is usually enforced by means of a chiral restraint (even if
the group in question is not chiral). You would need to calculate the
expected chiral volume of the C atom for the target position of the O
atom.
Che
Hello all,
We would appreciate your help on an error message one of our graduate students
has encountered using Xfit in CCP4. You can respond to him directly at:
[EMAIL PROTECTED]
Thank you
Mona Rahman
Forwarded Message
---
On Thursday 04 December 2008 11:50:30 Huiying Li wrote:
> Thank you all for suggestions and explanations. I did not make it clear. The
> tilt angle I wanted to restrain is the one from a C-OH bond to a plane
> (The C is in the plane). The O atom of OH group is not in the planar
> restraint in th
Thank you all for suggestions and explanations. I did not make it clear. The
tilt angle I wanted to restrain is the one from a C-OH bond to a plane
(The C is in the plane). The O atom of OH group is not in the planar
restraint in the cif file. At 2.1A I can "see" the feature of tilting of
this
Hi Tim,
The Shimadzu UV2401PC comes at a reasonable price and has all features you
might possible need in a
Biochemistry lab. And if you like the option to use small sample volumes, I
would suggest to by a TrayCell
from Helma - you put it in a regular photometer, it guides the light throug
If you reduce the path by a factor of 50, can you not increase the
concentration by the same factor without violating the shadowing
assumption?
Mike
On Thu, Dec 4, 2008 at 10:48 AM, Patrick Loll <[EMAIL PROTECTED]> wrote:
> At the risk of dragging this discussion even further afield from
> cryst
We too have a nano-drop. We really like it , but have not yet fully
switched over.
I agree with all the good things said about it , but here are the few times
the nano drop falls short:
1) We still use the old spec ( 1 cm path length ) for things at a very low
concentration , i.e for the monitor
Wow, that's like putting a pool in your backyard so you don't have to
pay the $3.00 admission every day (I'm kidding). In any event, Ocean
Optics has some very nice, small, and portable units that would run
around $3000 total. These connect to the USB port in a computer and
produce data that
One more issue regarding the Nanodrop: one has to work quite quickly
to avoid potential evaporation. Before buying such an instrument, I
would strongly recommend a demo and careful comparisons between the
Nanodrop and a good, conventional spectrometer with a representative
range of samples.
At the risk of dragging this discussion even further afield from
crystallography:
How can you get realistic numbers for concentrated solutions using
the Nanodrop? I understand that the instrument reduces absorbance by
using a very short path length. However, I thought that in order for
t
We also like the Nanodrop. Very fast, no cuvettes (breaking, washing,
cleaning, uh nitric acid bath anyone?), and the .ndv data file is a
delimited text file. Open in a text editor, copy and paste into a
spreadsheet, and you have a convenient record of all of your stocks,
including date, sample n
A postdoctoral position in macromolecular crystallography is available
at the three Cassiopeia beamlines at Max-Lab in Lund, Sweden, for a
period of two years starting as soon as possible. The Danscatt
consortium (www.danscatt.dk) is funding the position, and the successful
candidate will work full
Hi Huiying
At 2.1A I would be very surprised if you see any density for the H atom
in which case the refinement is not going to move it out of the plane
whatever weight you give the torsion restraint. To answer your earlier
questions the period of a torsion restraint is the number of energy
minim
CCP4 bulletin board wrote on 12/04/2008 10:16:02
AM:
> Dear all,
>
> we would like to purchase a UV spectrometer for measuring protein
> concentrations (280nm), and I would like to here your comments and
> especially recommendations.
>
> We don't need anything fancy, a small, fast device would be
We use a Beckman Coulter DU730. It has a small footprint if lab space is an
issue. It will do single-wavelength, multi-wavelength, or take an entire
spectrum in 0.5 nm steps if you desire. It comes with the standard 1 ml
cuvette holder, but we also purchased the microcuvette accessory for volume
Acturally, I want to find a way to keep the OH tilted out of the
neightbouring plane by about 10 degrees. At 2.1A resolution the REFMAC
refinement tends to refine it into the plane even though I have included
torsion angle restraint in the library for the ligand. I thought I could
play with the
I would also recommend the nanodrop. It takes a whole spectra every
measurement and there is no need to dilute your sample. You can demo it for
a week and try it out.
James M. Vergis, Ph.D.
University of Virginia Molecular Physiology and Bi
Tim - I would recommend a spectrometer that records entire spectra,
instead of one that takes readings at just 280 nm. Contributions from
light scattering can be very strong and can give results that deviate
from the true value by a factor of two or more. One cannot detect
scattering withou
Dear Tim --
On 4 Dec 2008, at 15:16, Tim Gruene wrote:
we would like to purchase a UV spectrometer for measuring protein
concentrations (280nm), and I would like to here your comments and
especially recommendations.
I love the Nanodrop system... I know you said you don't want anything
fan
Dear all,
we would like to purchase a UV spectrometer for measuring protein
concentrations (280nm), and I would like to here your comments and
especially recommendations.
We don't need anything fancy, a small, fast device would be sufficient.
Tim
--
Tim Gruene
Institut fuer anorganische Ch
Dear Deb,
We've seen the detrimental effects of local disorder time and tme again.
So - yes it is very likely that the putative disordered loops
detrimentally affect the quality of your crystals.
You can try to engineer your protein to be better - it usually takes a
number of internally engineere
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
I have to apologise: For some reason I assumed that the ccp4-server (or
the people who package the suite) was located in York, which - as I have
been pointed out to - is not true. I would like to apologise for my
prejudice. Anyway I did not mean to
Hi Tim,
You are the third person to make this very sensible suggestion. Once we
actually release the software we will be sure to do this! The limiting
step at the moment is that many small changes are going in (you will
have noticed the absence of a release announcement) which of course
change the
PREDOCTORAL POSITION IN STRUCTURAL BIOLOGY
Applications are invited for a PhD position within Prof. Miquel Colls
laboratory at the Institute for Research in Biomedicine / Institut de
Biologia Molecular de Barcelona (CSIC) to work on the Project Estudio de
Proteínas de unión a DNA. The position
A fast and simple method to check whether the downloaded file is corrupt
is to calculate checksums, e.g. md5 or sha - corresponding programs should
be available on most Unix/ Linux systems. It depends, however, on York
calculating the checksum and putting it next to the actual archive for
downl
Hi Wim,
I think that the main question I would ask is how you calculate the
Wilson B factor with 3.0-3.5 A data ...
We have done a rather big study of about 12,000 structures and below
2.5 A, how you calculate the B can result to
major discrepancies. There is hardly a line to get the gradient
Dear Michael,
How did you do the download? I have just downloaded this file using the old
fashioned command line ftp method, and it worked fine. I expect that there has
been an error somewhere in the transmission.
If you fetch the file from:
ftp ftp.ccp4.ac.uk
cd ccp4/6.1
get ccp4-6.1.0-core-s
Dear Charles,
to your information:
I just downloaded the Version 6.1 source tar file to my x86_64 Linux box
(SuSE 10.2, AMD64) and got the following tar error message.
All other (LINUX-386 and both COOCH and PHASER) tar files were fine!!
---> SNIP
...
ccp4-6.1.0/lib/data/monomers/ps.resource
ccp
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