Re: [ccp4bb] Off-topic: ELNs
Hi Seiji, I would recommend Labguru (www.labguru.com) which is cloud-based ELN and laboratory management solution. This tool encompass the management of experiment and projects, connects between experiments and individual samples, manages the different storage facilities down to the single tube and inter-connects the knowledge base of your labs (protocol, articles) to every experiment/project. There are both free accounts (for individual students in the lab) or paid accounts for whole lab solutions, which take use of labguru's sharing capabilities among users. The system comes with a fast and reliable human support. Take care, Chen --- Chen Guttman The Zarivach laboratory for Macromolecular Crystallography Building 39, Room 009B Ben-Gurion University of the Negev POBox 653 Zip Code 84105 Beer-Sheva Israel http://lifeserv.bgu.ac.il/wb/zarivach Tel. +972-8-6479519 Fax. +972-8-6472970 On Mon, Jan 16, 2012 at 23:28, Seiji Sugiman-Marangos wrote: > Hi, off-topic question regarding electronic laboratory notebooks. Our > lab is planning on moving from paper to digital record keeping and I > was wondering which of the available ELN platforms are being used by > the ccp4 community. > > We are primarily a crystallography lab but we would also need some > versatility in the platform as some of our lab members are more focused > on biochemistry. > > Any suggestions or comments would be greatly appreciated! > > Thanks, > Seiji >
[ccp4bb] French Press valve replacement
Dear CCP4 users, I apologize for the non-crystallography question. Our French Press valve have just been broken and we are looking for a replacement (see link for valve's image): http://www.cgp.co.il/Documentary/Zarivach-Lab/Misc/i-rcxfFhp/0/M/French-Press-Valve-M.jpg Please email me or zarivach[at]bgu.ac.il in case someone has such a replacement valve. Thank you, Chen --- Chen Guttman The Zarivach laboratory for Macromolecular Crystallography Building 39, Room 009B Ben-Gurion University of the Negev POBox 653 Zip Code 84105 Beer-Sheva Israel http://lifeserv.bgu.ac.il/wb/zarivach Tel. +972-8-6479519 Fax. +972-8-6472970
Re: [ccp4bb] Crystal structure and NMR structure
Here you go: http://www.ncbi.nlm.nih.gov/pubmed/12015150 Domain swapping of Cyanovirin. Chen --- Chen Guttman The Zarivach laboratory for Macromolecular Crystallography Building 39, Room 009B Ben-Gurion University of the Negev POBox 653 Zip Code 84105 Beer-Sheva Israel http://lifeserv.bgu.ac.il/wb/zarivach Tel. +972-8-6479519 Fax. +972-8-6472970 On Sat, May 21, 2011 at 08:34, Vandu Murugan wrote: > Dear all, >I would like to get some information on proteins where there is > conformation/structural change between the crystal structure and solution > structure of the same protein. Do anybody came across such situations? > Thanks in advance.. > > cheers, > Vandu >
Re: [ccp4bb] Reproducing crystals.
Hey Jun, If it's an old batch check and see if you have microorganisms living in the stock or proliferating in the drop - see the paper by Bai et al: doi:10.1107/S1744309107002904 In this paper they demonstrated how they could not reproduce a crystal hit from an old screen up until they realized a fungi that grew in the drop has been secreting protease that chewed up certain part of their protein - once they have utilized in-situ proteolysis they managed to reproduce there crystals with their home-made ingredients and, of course, solve the structure. In line with this, and if it is possible, pickup one of those crystals and run it on a gel as they did so to make sure it is in the correct size and not a truncated version. Good luck, Chen --- Chen Guttman The Zarivach laboratory for Macromolecular Crystallography Building 39, Room 009B Ben-Gurion University of the Negev POBox 653 Zip Code 84105 Beer-Sheva Israel http://lifeserv.bgu.ac.il/wb/zarivach Tel. +972-8-6479519 Fax. +972-8-6472970 On Tue, Apr 12, 2011 at 13:56, Jun Yong Ha wrote: > Hi all, > > Recently, I produced crystals with MBClass1-64 which contains PEG4000, > HEPES-Na and NaCl. But, I struggled to reproduce crystals. I tried to set up > tray with different batch of solution. I got the crystals only from 2008 > solution, but not from fresh ones. I asked technical service of Qiagen, but > they did not have any stock. > > pH between fresh and old solution is the same. I could reproduce crystals > with this old solution 100% when setting up. > > Do you have any experience like this? Is PEG4000 degraded or oxidized? > > Please help me. > > Thanks in advance. >
Re: [ccp4bb] Tev Cleavage issue !!
Hey Anita,
I would like to add to Artem's comment that you can also try and cleave the
protein at 30c for 2hr and then continue the cleavage overnight at 4c (you
should check and see that your protein can withstand 30c incubation for 2hr,
of course).
In regard to your non-diffracting crystals - you can try seeding: Streak or
Macro-seed your crystals onto a screen ("screen seed") or onto the same
conditions in which the crystals grew. Sometime you might get different
morphologies that might diffract.
Good luck,
Chen
---
Chen Guttman
The Zarivach laboratory for Macromolecular Crystallography
Building 39, Room 009B
Ben-Gurion University of the Negev
POBox 653
Zip Code 84105
Beer-Sheva
Israel
http://lifeserv.bgu.ac.il/wb/zarivach
Tel. +972-8-6479519
Fax. +972-8-6472970
On Fri, Apr 8, 2011 at 04:37, anita p wrote:
> Hi Crystallographers,
> I am working of 23 Kda protein with a Nterminal His tag and a TEV
> cleavage site.
> I am getting crystals with the his tag and tev site intact, but they dont
> diffract.
> *Is it probable that they dont diffract because of the extra his tag and
> the tev site?*
>
> I am trying to get rid of this tag but the reaction is optimum at 10:1
> protein to TEV ratio in micrograms overnight incubation without shaking.
> I tried to run it on histrap column after this reaction but I am not able
> to purify cleaved protein from TEV and uncleaved.
> I have tried several times but I get 3 bands ie., the TEV, uncleaved and
> Cleaved.
> I have also tried to use the Nibeads instead of the histrap column, but no
> difference is seen.
> * Is there a possible way to approach this problem?*
>
> Suggestions awaited
> Anita
>
