Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread Daniel Picot
Hi Frank, 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

Re: [ccp4bb] preparation of citrate buffer pH3-6.5

2014-01-30 Thread Daniel Picot
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. Daniel 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

[ccp4bb] Meeting announcement Dynamo Paris 2014

2014-02-04 Thread Daniel Picot
but mandatory before February 15th on the web site. Daniel Picot

Re: [ccp4bb] Se-Met and disulfides

2014-02-27 Thread Daniel Picot
Hi Reza, You have here an example of MAD data collected fromoxidized and reducedselenomethionine-containing protein: 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,

Re: [ccp4bb] Invisible atoms in ligands

2014-06-16 Thread Daniel Picot
Dear Ian, 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

Re: [ccp4bb] phaser oprn error

2007-03-26 Thread Daniel Picot
You may have called the version of phaser installed in the phenix path. Type wich phaser in a terminal to check it. Daniel yang li a écrit : Hi: I am using CCP4 6.0.2, it has phaser contained in this package. When I use it to do mr, error occured:

Re: [ccp4bb] water soluble protein that needs detergent to be stable

2007-08-29 Thread Daniel Picot
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 crystallisation,

Re: [ccp4bb] His tag on membrane protein

2007-11-23 Thread Daniel Picot
Hi Deliang, 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

Re: [ccp4bb] Color of heme containing Xtals

2008-03-13 Thread Daniel Picot
Jan, 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. Daniel Ian

Re: [ccp4bb] metal-chelating affinity chromatography and FosCholine detergents

2010-07-13 Thread Daniel Picot
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 purification yield

Re: [ccp4bb] Fwd: [ccp4bb] XSCALE

2010-08-05 Thread Daniel Picot
Another very nice script to run and collect statistics from XDS is xdsme from Pierre Legrand http://code.google.com/p/xdsme/ Daniel 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

Re: [ccp4bb] Why appear the grid on the low resolution areas

2010-09-14 Thread Daniel Picot
Dear Xingliang, 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

Re: [ccp4bb] heterologous seeding

2010-09-22 Thread Daniel Picot
An old one: Eichele G, Ford GC, Jansonius JN. Crystallization of pig mitochondrial aspartate aminotransferase by seeding with crystals of the chicken mitochondrial isoenzyme. J Mol Biol. 1979 Dec 5;135(2):513-6. PubMed PMID: 537086. Daniel Le 21/09/2010 22:24, Christopher Rife a écrit :

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Daniel Picot
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

Re: [ccp4bb] hydrohyapatite column

2010-11-30 Thread Daniel Picot
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. Daniel Le 29/11/2010 16:08, Sebastiano Pasqualato a écrit : Hi all, I read/heard that

Re: [ccp4bb] off topic: GPCR membane insertion/orientation

2011-03-04 Thread Daniel Picot
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

Re: [ccp4bb] nmr blog

2012-03-23 Thread Daniel Picot
You can find here several links concerning NMR http://www.drorlist.com/nmr.html with a discussion list: https://listes.sc.univ-paris-diderot.fr/sympa/info/nmr Daniel Le 22/03/2012 19:35, Luthra,Amit a écrit : Is any NMR blog available for discussion? Amit Luthra, Ph.D. Post-Doctoral

Re: [ccp4bb] DDM

2012-03-27 Thread Daniel Picot
It is important to distinguish between the solubilisation and the purification steps: 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

Re: [ccp4bb] Pictures of DDM crystals?

2009-08-11 Thread Daniel Picot
Hi Joe, 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

Re: [ccp4bb] rigaku micromax 007 cooling

2014-07-24 Thread Daniel Picot
Dear Andreas, 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. Daniel Le 24/07/2014 17:53, Andreas Förster a écrit : Dear all,

Re: [ccp4bb] In search of an article

2014-11-03 Thread Daniel Picot
Hi Phhilippe, T. Y. Teng, J. Appl. Crystallogr. 23, 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

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

2016-12-14 Thread Daniel Picot
Veni vidi 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 Daniel 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