Ethan Merritt wrote:
Please also have a look at
A Olczak, M Cianci, Q Hao, PJ Rizkallah, J Raferty, JR Helliwell (2003).
S-SWAT (softer single-wavelength anomalous technique)
Acta Cryst. A59, 327-334.
in which the authors show several derivations for the estimated
anomalous signal, based
As far as I know the compatibility has been broken because
of adding new features such as intensity based refinement
or multiple anomalous scatterers to the GUI
Pavol
--
Sent from: Leiden ZH Netherlands.
This is VERY VERY VERY irritating!
Why has it been allowed...
Is there any
Hi -
I must agree that if one RTFMs its clear. Now, back to the real world.
My experience is that most SCALA users tend to look at I/sigmaI.
I admit that I had been using that for deciding data cutoff, many
times, but thats another discussion.
The vast majority of Table 1 I see report
Dear all,
I am terribly sorry about my mis-directed email.
Please accept my sincere apologies.
Manfred.
--
* *
*Dr. Manfred S. Weiss
Postdoctoral Vacancy
Research Associate
A Wellcome Trust funded postdoctoral position is available to work with Dr
Matt Higgins in the Department of Biochemistry, Cambridge University on
the structural biology and biochemistry of cell surface proteins involved
in severe and cerebral malaria.
Hi Tassos,
It's a bit early in the year to have our annual I/sigI discussion on the
CCP4BB, isn't it?
Usually, we wait until at least April 1. :-)
.
d*TREK could confuse people further as to which one should be used for
reporting and decision making.
.
The Big Question Again:
I am refining my crystal structure in which I have two identical
chains in one asymmetric unit.
Space group is H32 and each chain yields me a biological trimer as expected.
The problem is, do I have to assume they are identical, or they are
really different.
After each cycle of refinement, if I
Dear all,
I would like to draw your attention to the following scientific event
in preparation:
Practical Workshop on Characterization of Protein Complexes in
Structural Biology EMBL-Hamburg, 30th June - 3rd July 2009.
The workshop is aimed at advanced graduate students and postdoctoral
Since Phil is generous enough to offer to rename the Mn(I/sd)
column to I/SIGMA
and maybe rename I/sigma to I/rms-scatter or so, if Jim could also
rename
one of his columns, and Wladek can add one, we can have a standard.
Or even better if everybody would use I/sigma(I) then we would
even
Dear Sang
They are really different!
And I guess you would probably want to use NCS restraints depending on
your resolution.
Regards,
Folmer
2009/3/24 Sang Hoon Joo s...@duke.edu:
I am refining my crystal structure in which I have two identical
chains in one asymmetric unit.
Space group is
Hello,
We can make a nice 1:1 complex between two proteins that then gradually
precipitates during storage at 4 degC. With 0.005% Tween-20 the complex is
stable and does not preciptate noticeably. We have used this in buffers to
measure the kinetics of binding by Biacore so it is clearly
Sang Hoon,
Each molecule in the asymmetric unit is most likely different. I work on a
protein that crystallizes as a homodimer with 2 molecules per asymmetric
unit and there are some differences between the two (eg: electron density
visible for the 14 N-terminal residues in one molecule, but not
Dear SHJ,
there is no reason to expect that the 3D structure of two molecules within
the same asymmetric unit are identical even if their chemical formula is
identical.
These two molecules experience slightly different crystal packing contacts
are are expected to be different. Obviously, in
Hi Darren,
I'm not aware of any (membrane) protein crystal structures solved with tween20.
It's heterogeneous, and its color suggests it contains impurities and/or
oxidation products, making it even more heterogenous. It would be better to
test the behavior of your complex in the presence of
Hi Sang Hoon,
You should do the refinement in BUSTER, which uses a novel method to
impose NCS restraints. These restraints (called LSSR restraints) were
designed specifically to provide an answer to your question in a
systematic way, by comparing the local environments of corresponding
Dear All,
I found this paper quite informative on the procedure for screening and
selecting detergents for protein crystallization.
http://journals.iucr.org/d/issues/2005/04/00/sx5021/sx5021.pdf
Best wishes,
Gordon
M. Gordon Joyce,
Visiting Fellow,
Structural Immunology Section,
Sang,
They are always different. But depending on your data/parameter ratio,
you may be better of assuming they are similar (with NCS restraints) or
even identical (with strict NCS). Ask to a friendly crystallographer
around you when employing NCS is good for you. Crystallographers with
high
Hi Darren
I believe that the most frequently used detergent for protein
crystallization (not including membrane proteins) is octyl-glucoside.
The most important parameter is the CMC of the detergent and the size of the
micelles of free detergent if you have micelles around. These considerations
do
Edward A. Berry wrote:
And what about different format of pucks/cassettes/tongs etc?
I can still read my old Vax backup tapes (on a linux box with an
exabyte tape drive), but my old Yale-style pins won't fit in the
Hampton Research cryotongs available at the beamline, they don't sit
well on the
Darren--
Last year I attended the Membrane Protein Crystallization Course organized
by Vivian Stojanoff at BNL. James Love talked about screening detergents
using ASEC, and we have set this up in our lab now (not as elaborate a
system used at the NYCOMPS). We use a universal buffer with a
So, yes, a universal pin solution exists, and the hardware is not
expensive, but I gave up a long time ago on trying to get
other beamline
scientists to expand their support of pin types. But this is
not to say
that there has not been progress. Aina Cohen I think
deserves a lot of
I have seen proteins refined as 'the same', modeled to an averaged map
etc only to have one of them with much higher Bj because most likely
they are NOT the same so watch out by treating them as 'the same' you
are losing the very valuable information that you might be looking for
Ewa
I would like to take the time to welcome all general users to the newest
beam lines at the Advance Photon Source, Life Sciences CAT Sector 21.
http://ls-cat.org http://protein.nsls.bnl.gov/
There is time available for rapid access, the dates are listed on the
website and users can subscribe for
I had a student solve a medium resolution (2.3 A)
data set with (unfortunately) 12 identical protein chains in the
asymmetric unit. To save a little time, and to take advantage of a
large amount of potential averaging we used NCS to do the initial phase
of the refinement. For 10 of the 12
I have a mtz from Autosol/resolve that has the following columns:
OVERALL FILE STATISTICS for resolution range 0.002 - 0.261
===
Col SortMinMaxNum % Mean Mean
Resolution Type Column
num order Missing complete abs.
Having dealt with quite a few cases of more than one molecule in the
AU (including a couple of dreaded 12-meric assemblies... bleah), I am
still looking for the best way to identify proper NCS operators for
the myriad of potential combinations of fragments.
As has been said, it is
Hi all,
I recently collected data at Argonne National Laboratories at BioCars
on the 14 IDB beamline. The detector is a mar 165 ccd detector. I
was unable to process my datasets at the synchrotron (HKL2000) hoping
to process them at home. However, I'm unable to display the frames
on
On Tuesday 24 March 2009 12:20:17 Mischa Machius wrote:
Having dealt with quite a few cases of more than one molecule in the
AU (including a couple of dreaded 12-meric assemblies... bleah), I am
still looking for the best way to identify proper NCS operators for
the myriad of potential
Dear Francis
You do not have to tell which columns were used for refinement. The
program should pick FP/SIGFP. You can deposit the foo.mmcif and your
coordinate to the PDB.
The alternative to convert/validate your mtz file is to use the server
http://pdb-extract.rcsb.org/auto-check/ . It is
home computers. I do have the current def.site from biocars downloaded.
The error that keeps coming up is No valid license for un-mar165. ERROR
CODE 5. We tried getting an additional license (from HKL2000) for the
particular detector but it still doesn't seem to work. Any
Assuming that you did everything else correctly (e.g. placed the new
cr_info file you got from HKL into /usr/local/lib), are you sure you
included un-mar165 in your info file? They have this mar option which
refers to MAR imaging plate detectors (except MAR345) and thus does
not cover CCDs
My favorite trick was to define domain-wise ncs restraints,
extensively minimize with and without them, then plot the
difference in real-space R factor per residue. Ones that jump
up when restrained are usually involved in crystal packing,
etc, and should be removed from the restraints.
In my
Hello Roger,
did you publish your results? Your case sounds very educational and might
be interesting for teaching purposes, so a reference would be a nice thing
to have.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 24
Lawrence Berkeley Laboratory
Postdoctoral Researcher
Job ID: 22539
Division: Physical Biosciences
Date Opened: 3/24/2009
Summary: A postdoctoral position is immediately available to study
structure and function of macromolecular complexes and enzymes using
X-ray crystallographic methods. This
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