Dear Sudhir,
A blob surrounded by three Asp residues looks like a positively charged ion.
What else (buffer, additives) is in your crystallization drop? I would also try
to fit cysteine/serine. At 2 Å you will quickly see whether or not this is
correct.
Good luck!
Herman
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Hallo ,
first build a poly-ALA stretch. In coot or O this is conveniently
achieved using baton-build mode. This should improve the phases. Then
look at the side chains.Turbo-frodo has got somehting like a slider that
shows the sequence on screen
Next MX-proposal application deadline: March 1, 2012 is approaching
See also:
http://www.bessy.de/boat/http://www.bessy.de/boat/www/
We kindly invite new MX-proposals for beamtime applications for the next
beamtime period.
In order to apply for beamtime, please register at the HZB on-line
Dear colleagues,
I would like to point your attention to the following job opportunity -
professorship/director (W3) - which is jointly offered by the Forschungszentrum
Juelich and Heinrich Heine University Duesseldorf, Germany:
http://www.nature.com/naturejobs/science/jobs/243931
The focus
On 02/10/2012 07:35 AM, intekhab alam wrote:
Hi all
I have a 3A dataset for a protein-protein complex. I have successfully
build the first protein and refined it to R/Rfree 24/28. I can see some
density for my second protein but the density is a bit noisy. I have
attached the coot image of the
BBSRC MRes/PhD Studentship: Structural studies of biofilm-associated
proteins from human pathogens
4 Years (MRes Medical and Molecular Biosciences followed by a
three-year PhD) or 3 Years PhD, depending on qualifications, funded by
Faculty of Medical Sciences and BBSRC at the UK/EU rate.
This
Dear all,
I have a anomalous dataset, processed in HKL2000. Scalepack outputs a
file containing the separately merged sets of the Friedel pairs I- and
I+ and their standard deviations sigI+ and sigI-. Scalepack does not
output the averaged intensities (Imean) and the standard deviations
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins can be considered freeze-frame snapshots of actual
conformations assumed in solution. In a way, the assertion seems
almost definitely
How could they not be snapshots of conformations adopted in solution?
James
On Feb 10, 2012, at 1:25 PM, Jacob Keller wrote:
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins
On Fri, Feb 10, 2012 at 12:29 PM, James Stroud xtald...@gmail.com wrote:
How could they not be snapshots of conformations adopted in solution?
Packing billions of copies of an irregularly-shaped protein into a
compact lattice and freezing it to 100K isn't necessarily
representative of solution,
How could they not be snapshots of conformations adopted in solution?
Let me clarify--sorry about that. Consider several structures of the
same protein solved under different conditions, or several homologs
solved under similar conditions, or both. Further, let's say some
structural element,
Hi Jacob,
Lorena Beese has a few systems where snapshots of reaction mechanisms
have been looked at structurally.
Here are two such papers:
Long, SB, Casey, P., Beese, LS (2002) The reaction path of protein
farnesyltransferase at atomic resolution. Nature Oct 10;
419(6907):645-50.
On 02/10/2012 03:25 PM, Jacob Keller wrote:
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins can be considered freeze-frame snapshots of actual
conformations assumed in solution. In a
I believe the most justifiable assumption one
can make is that crystal structures are likely to represent the
least soluble conformations of a protein under the conditions of
crystallization (which might be a broad range of conditions,
including physiological).
Interesting to juxtapose these two responses:
James Stroud:
How could they not be snapshots of conformations adopted in solution?
David Schuller:
How could that possibly be the case when any structure is an average of all
the unit cells of the crystal over the timespan of the diffraction
So the implication is that some of these treatments might allow the protein to
overcome energetic barriers that are prohibitive in solution--after the protein
is already in the solid state and not in solution any more?
Another view is that crystallization is a result of stabilizing
Packing billions of copies into a compact lattice
Not so compact there is 40-80% water
freezing it to 100K
We have frozen many times protein solutions in liquid nitrogen and then thaw
and were working OK
non-physiological amounts of salt and various organics
What is the amount of salt and
Hi,
I have run ccp4 without issue on my OS X machine until recently. For some
reason I am not able to create new project directories, and therefore am not
able to run routines. The message that I am getting is the following: ERROR
saving parameters to file .../.CCP4/unix/directories.def I have
The contrast seems to boil down to the semantics of the word snapshot.
In my definition, I assume that the uncertainty of a structure is an intrinsic
quality of the structure and thus included in the meaning of snapshot. Part
of that uncertainty comes from averaging.
James
On Feb 10, 2012,
On Friday, February 10, 2012 12:51:03 pm Jacob Keller wrote:
Interesting to juxtapose these two responses:
James Stroud:
How could they not be snapshots of conformations adopted in solution?
David Schuller:
How could that possibly be the case when any structure is an average of all
the
Just to clarify - I actually think the original assumption that Jacob
posted is generally reasonable. But it needn't necessarily follow
that the conformation we see in crystal structures is always
representative of the solution state; given the extreme range of
conditions in which crystals grow,
Along the lines of Roger's second point, there was a very nice paper a few
years back that found very good agreement between the conformational ensemble
sampled by ubiquitin in solution (by NMR) with the ensemble of conformations
observed in a large number of crystal structures:
Lange OF,
Isn't calcium-calmodulin one of the archetypical examples of the
crystal structure probably not representing the solution structure
(perhaps because the crystallization pH = 4.5)? Look at that linker
helix--how stable can that be in solution? I don't think a single one
of the NMR ca-calmodulin
Hi Nat,
there are a number of viruses in which a domain swap occurs inside the
capsid, with the hinge sequence being highly conserved among their
respective families. Perhaps I'm missing your point, but I won't attribute
that kind of domain swap to any sort of crystal packing artifact.
Jon
Hi Jacob,
For Ca2+-CaM, and flexible proteins in general, the average conformation
in solution may differ from the most crystallizable conformation. However,
any crystallized conformation had to be sampled in solution at some point
in order to form a crystal, and thus the crystal structure
Hi,
There is a interesting paper/tool that might shed a little light on the
debate here:
The paper: http://www.ncbi.nlm.nih.gov/pubmed/19956261
The tool:
http://ucxray.berkeley.edu/ringer/Documentation/ringerManual.htm#Utility
As I remember, this tool claimed to be able to extract information
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