[ccp4bb] Postdoctoral fellowships in structural biology at Heidelberg University Biochemistry Center

2012-02-01 Thread Klemens Wild
*Postdoctoral Fellowships: Structural Biology / Molecular machines in protein targeting and ribosome biogenesis* The lab of Prof. Irmi Sinning at the Biochemistry Center (BZH) of Heidelberg University seeks to recruit 4 outstanding postdoctoral researchers for a period of 2--5 years. BZH is

[ccp4bb] 2nd Annual CLS Mx Data Collection School

2012-02-01 Thread Shaun Labiuk
The Canadian Macromolecular Crystallography Facility (CMCF) is excited to announce an intensive 5-day hands-on synchrotron data collection school at the Canadian Light Source (CLS) in Saskatoon. The School will take place June 5 - 9, 2012. Participants will attend a series of lectures and be

[ccp4bb] synchrotron X-ray picture

2012-02-01 Thread Patrick Loll
Hi all, I have a vague memory of having a picture in someone's presentation once, showing a smoking hot X-ray beam emerging from the beam pipe in a hutch at a synchrotron. I think the picture might have been a double exposure, with a long exposure that captured air ionization superimposed on a

[ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Dianfan Li
Dear all, Sorry about a non-crystallographic question here. I am working on a kinase and would like to get an ATP analogue into the crystals. When soaked with AMP-PCP, the kinase crystals crack in about 15 min at 4 C. I could try other analogues like AMP-PNP etc, but those would probably

Re: [ccp4bb] synchrotron X-ray picture

2012-02-01 Thread Matthew Franklin
Hi Pat - I, too, have a memory of such a picture. This isn't quite the one I was thinking of, but it should hopefully serve the purpose: http://www.nsls.bnl.gov/about/imagelibrary/images/hr/Synchrotron_Light2_hires.tif (there are a couple more from the parent page:

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Nat Echols
On Wed, Feb 1, 2012 at 11:17 AM, Dianfan Li l...@tcd.ie wrote: I am working on a kinase and would like to get an ATP analogue into the crystals. When soaked with AMP-PCP, the kinase crystals crack in about 15 min at 4 C. This isn't too surprising; most kinases undergo global conformational

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Fischmann, Thierry
Dianfan Some kinases have such conformation in non-activated apo form that the ATP binding site is partially obstructed. Soaking an ATP analog may then have 3 outcomes: 1) successfully open up the binding site without damage to the crystal, 2) fail to open up the active site and the compound

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Francis E Reyes
On Feb 1, 2012, at 12:17 PM, Dianfan Li wrote: I am working on a kinase and would like to get an ATP analogue into the crystals. When soaked with AMP-PCP, the kinase crystals crack in about 15 min at 4 C. 15 minutes is a long time. Scoop crystals during that time period. Do the cracked

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Artem Evdokimov
I assume that cocrystallization has failed? What you are experiencing is likely the effect of conformational transition caused by ligand. You can try very slow adition (even microdialysis) or if your ligand is fairly insoluble then you can just add a tiny solid particle of inhibitor to your drop

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Boaz Shaanan
Hi, First, it's very much a crystallographic question. Second, the success or failure in soaking in ligands/cofactors depends quite often also to the crystal packing. Some packing forms (and the spacegroups that go with it) will tolerate the soaking even if it's accompanied with a

[ccp4bb] Subject: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Pascal Egea
Hi , To add to the previous comments, crystallization of GTP or ATP (or their analogues) with their kinase/ A- or G-tpases can depend on a lot of factors that were mentioned (such as packing). A simple common problem is that ATP solutions should be carefully buffered prior to their use for

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Sofia Caria
Dear Dianfan, In some cases the ATP-lid of the kinase is blocking the active site in the crystal form. In those cases the only option is to try co-crystallisation. Besides ATP and the homologs you mention you can also try ADP that as you will see in the PDB has been heavily used for kinases.

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Yuri Pompeu
Maybe someone has suggested this already... If so, I am re-enforcing it. If the cracking is coming from actual molecular movement induced by binding (and not other reason like differing ionic strength in your soaking conditions) you could try setting up some co-crystallization and (hopefully)

[ccp4bb] On sodium malonate

2012-02-01 Thread Dialing Pretty
Dear All, For the 3.4 M sodium malonate of Hampton Research, will you please tell me how the pH was regulated to 6.0, 7.0 and 8.0 separately? Cheers, Dialing

Re: [ccp4bb] On sodium malonate

2012-02-01 Thread Doug Ohlendorf
Dialing, Malonic acid is dissolved in water and then pH adjusted to the desired value with NaOH. Caution: dissolving malonic acid is highly exothermic. Do it slowly, in a hood. Doug From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dialing Pretty Sent: Wednesday,