Re: [ccp4bb] effective iodide conc. for SAD data

Dear All, I really thank everyone who gave me excellent suggestions. I will try them to see which one works better for me and my crystals. Again thanks a lot for your help. Regards, Rajesh Date: Thu, 3 May 2012 20:56:21 +0200 From: florian.sa...@embl-hamburg.de Subject: Re: [ccp4bb] effective i

Re: [ccp4bb] How to overlap DNA

Dear Guys, Thank you very much for your suggestions! I have tried Superpose from CCP4i as suggested by Arka& Nicolas. It works fine and can overlap the whole base as the LSQ in coot. The USF (lsqman suggested by Tim)has not been installed in my PC and I will try it and see after it has been install

[ccp4bb] new fragment library

Hi -Sorry for the slight off-topic. Passing along that we have a new fragment library - called library 2 (the other was library 1). Same format, dry films in 96 well plates. The library includes additional more specialized cores which we think nicely complement library 1. Some have also asked

Re: [ccp4bb] effective iodide conc. for SAD data

Yes I did and could solve the structure by SAD. In total 8 I atoms found. 6 bound at anion binding sites. 2 as I2. None covalently bound to tyrosine. Florian Am 03.05.12 19:42, schrieb Edward A. Berry: > Did you locate the Iodine(s)? Did you have iodotyrosine, or I^- bound > at anion binding si

Re: [ccp4bb] effective iodide conc. for SAD data

Did you locate the Iodine(s)? Did you have iodotyrosine, or I^- bound at anion binding sites? There are two distinct methods based on I2/I-. Florian Sauer wrote: Dear Rajesh, another method to incorporate Iodine into your crystal is by simply placing a drop of KI/I2 solution next to the cryst

Re: [ccp4bb] effective iodide conc. for SAD data

Dear Rajesh, another method to incorporate Iodine into your crystal is by simply placing a drop of KI/I2 solution next to the crystallization drop. Have a look here: Acta Cryst. (2006). D62, 280-289 New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen pe

Re: [ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker & Fractionator

Or make it yourself if you got time. Anal Biochem.1994 Sep;221(2):397-400. A syringe-based gradient former for linear and exponential gradients. Shearer G Jr

Re: [ccp4bb] effective iodide conc. for SAD data

Please see my poster at the ACA 2012 meeting. See also: (1) Dauter, Z., Dauter, M. & Rajashankar, K.R. (2000) Acta Cryst. D56, 232-237. (2) Nagem, R.A.P, Dauter, Z. & Polikarpov, I. (2001) Acta Cryst. D57, 996-1002. :) From: CCP4 bulletin board [CCP4BB@JISCMAIL.A

Re: [ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker & Fractionator

In US Fisher Scientific sells CBS scientific , California different ranges of gradient maker. I especially found them useful for my use for density gradient centrifugation. the material used in the manufacture is clear and easy to clean each time. It is kind of not very controlled automatically but

Re: [ccp4bb] effective iodide conc. for SAD data

Interesting idea. The only caveat that springs to mind is that the more useful anions (e.g., iodide and bromide) are on the chaotropic end of the Hofmeister series and may potentially destabilize protein structure or protein-protein interactions, which might complicate co-crystallization starti

[ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker & Fractionator

Dear all, I find myself working on a number of large multi-protein complexes, and am likely to need to use Sucrose / Glycerol gradients in preparing them. IWhilst I can do this manually in the short term, I was wondering if someone could recommend any manufacturer's (preferably Europe/UK based

Re: [ccp4bb] effective iodide conc. for SAD data

I have wondered for a long time now why it is not standard practice for all crystallization protein stocks to contain either Br- or I- ions instead of Cl-, even for cationic buffers like TRIS, which could be titrated with HBr or HI to get in the 10+ mM range. Also, one could use Cs or Rb for the ca

Re: [ccp4bb] effective iodide conc. for SAD data

Rajesh, Why not try a soak-in-place by adding iodide and/or cryoprotectant directly to the crystallization drop? Then you only have to fish out the crystal once, minimizing handling. I usually do this by preparing an artificial mother liquor solution that has 125% of the final desired concent

Re: [ccp4bb] effective iodide conc. for SAD data

Iodide is a fantastic derivative. One does not need a lot with modern X-ray equipment, careful data collection, and great software. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh Kumar [ccp4...@hotmail.com] Sent: Thursday, May 03, 2012 8:5

[ccp4bb] PhD Position at the Institut de Biologie Structurale Jean-Pierre Ebel Grenoble

PhD Position at the Institut de Biologie Structurale Jean-Pierre Ebel Grenoble A PhD position is available in the Synchrotron Group headed by Dr Jean-Luc Ferrer at the Institut de Biologie Structurale (IBS) at Grenoble, starting in Autumn 2012. IBS is close to the European large instruments, the

Re: [ccp4bb] effective iodide conc. for SAD data

Hi Rajesh, it can be a bit all over the place: For quick soaks, we typically use 500mM-1000mM. A good starting point might be to simply replace the NaCl concentration in your protein buffer. By some serendipity we also managed to solve a structure by I/S SAD after a 1mM NaI soak. One iodide had

[ccp4bb] effective iodide conc. for SAD data

Dear All, I have very thin crystals but diffracting. I was not able to handle them easily for iodide soak. I always lost the crystals during manipulation and other big crystals obtained after seeding doesn't even give any diffraction. I tried for co-crystallizing with NaI. The crystals appear o

[ccp4bb] Beamline Scientist (I03) position available at DIAMOND

Dear all, Following from Martin's post yesterday, we also have a beamline scientist vacancy at Diamond to join the I03 beamline team. I03 provides a facility for the determination of biological macromolecules using X-ray diffraction. The beamline is equipped with a state of the art experimental

Re: [ccp4bb] how to overlap DNA

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear leo, how do you mean 'not perfect'? Superposition is not too difficult a task once you have defined the atoms you want to superpose and there should not be much variation. You could fine-tune your result with lsqman (USF program suite) which all

Re: [ccp4bb] how to overlap DNA

Dear Leo, I use "*superpose*" included in the ccp4 programms suite. You can manage a lot of parameters. In my case for exemple, i use the "superpose specified atoms/residues" I defined the model which move et the one wich is the reference. I precise the residues range (in DNA case residue me