I wil have to change my advices and lectures: go and look at the Uppsala
Electron Density Server EDS
It has been extremely useful.
Even sometimes vici
Le 13/12/2016 à 19:52, Patrick Loll a écrit :
Ave atque vale.
The EDS was hugely useful (and will continue to be so in its
T. Y. Teng,
J. Appl. Crystallogr.
J. Appl. Crystallography 23:387–391 (1990)
Mounting of crystals for macromolecular crystallography in a
free-standing thin film
A method for mounting single crystals in macromolecular crystallographic
studies is described in which the
We have a Hyfra water cooled system (VWK50) on our MicroMax 007,
but it is probably over-dimensioned
because it is also used by a Xstream equipment, a smaller dedicated
cooler to the micromax could be better.
Le 24/07/2014 17:53, Andreas Förster a écrit :
This has been discussed in a review and related articles by Brian
Matthews and Liljun Liu:
Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins
really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review.
PubMed PMID: 19241368; PubMed
You have here an example of MAD data collected fromoxidized and
It states :phasing power of theoxidized data is doubled for the dispersive
signal and is 20% stronger
for theanomalous signal at the peak wavelength
Thomazeau K, Curien G,
but mandatory before February 15th on the web site.
But you have to be aware that pH depends on the concentration of the
buffer. This is especially the case for phosphate and citrate buffer.
Le 30/01/2014 15:51, Schnicker, Nicholas J a écrit :
It’s a pain but I usually just make each pH of whatever buffer I’m
using (if you make it
Do not forget that membrane protein crystals are often fragile and
difficult to manipulate.
Finding good cryo condition can be difficult and small temperature
variation can destroy crystals
within minutes, this makes room temperature diffraction tests not always
obvious. The time
It is important to distinguish between the solubilisation and the
1) During the solubisation step you need to care about the
lipid/detergent ratio. The amount (not the concentration) of detergent
(i.e. in non monomeric form, the detergent above the cmc) is important.
You can find here several links concerning NMR
with a discussion list:
Le 22/03/2012 19:35, Luthra,Amit a écrit :
Is any NMR blog available for discussion?
Amit Luthra, Ph.D.
In addition to Bert remarks, you can read this paper from the positive
inside rule instigators.
Seppälä S, Slusky JS, Lloris-Garcerá P, Rapp M, von Heijne G. Control of
membrane protein topology by a single C-terminal residue. Science. 2010
Jun 25;328(5986):1698-700. Epub 2010 May 27. PubMed
Hydroxyapatite can be miraculous, but is often very capricious: among
others, it is temperature sensitive and two different corners of a
somewhat inhomogeneous cold room may provide different results.
Le 29/11/2010 16:08, Sebastiano Pasqualato a écrit :
I read/heard that
Here is an example that is is not cryocongelation but spacegroup change
upon cooling :
Garavito RM, Jenkins J, Jansonius JN, Karlsson R, Rosenbusch JP. X-ray
diffraction analysis of matrix porin, an integral membrane protein from
Escherichia coli outer membranes. J Mol Biol. 1983 Feb
An old one:
Eichele G, Ford GC, Jansonius JN. Crystallization of pig mitochondrial
aspartate aminotransferase by seeding with crystals of the chicken
isoenzyme. J Mol Biol. 1979 Dec 5;135(2):513-6. PubMed PMID: 537086.
Le 21/09/2010 22:24, Christopher Rife a écrit :
This is vaguely reminiscent to a pattern that was observed by Zora
Markovic-Housley on precession picture of crystals of ornithine
aminotransferase: the even layer (l=2n) had a nice pattern diffracting
to high resolution while the odd layer (l=2n+1) had a honeycomb
Another very nice script to run and collect statistics from XDS is
xdsme from Pierre Legrand
Le 05/08/2010 16:55, Jovine Luca a écrit :
WRT the redundancy, I am afraid you have to recompute an approximate value
yourself using the number of
A crude purification prior loading the metal-chelating column (like ion
exchange chromatography) can help and speed up the binding to the column
(remark not specific to Fos-cholin). Fos-choline is, contrary to
popular belief, a quite harsh detergent and this may affect the
It is often useful to prepare in parallel drop without protein but with
a large excess of detergent and protein buffer: a typical membrane
protein of ca 100 kDa will bind something like 100-200 molecules of DDM,
If you want to match the quantity of detergent that is bound to a 10
Crystals containing haem protein are not necessarily red, the colour
depends on the oxidation state of the haem and on the haem/protein
ratio. A FeIII haem will look yellowish, gold or brown depending on
the haem/protein ratio, while an FeII haem will look more pink or red.
We have crystallized the complex cytochrome b6f with an extension of
His6 (no linker) at the c-terminal of cytochrome f (Stroebel, 2003). The
His extension takes part to the crystal contacts. The electron density
is visible but not very well defined. We have not tried to remove the
I have not dealt myself with this type of protein, but Alex McPherson
tested the detergent beta-octylglucoside (at a concentration of 1.5 %,
i.e. above the cmc) for the crystallisation of soluble protein and tRNA
(1986, J.Biol.Chem 261:1969-75), the detergent did not hampered the
You may have called the version of phaser installed in the phenix path. Type
in a terminal to check it.
yang li a écrit :
I am using CCP4 6.0.2, it has phaser contained in this package. When
I use it
to do mr, error occured:
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