Re: [ccp4bb] SUMMARY: losing zinc during crystallization

Hello I wish to thank everyone for all the helpful replies. A summary follows: While some expressed surprise at the zinc lability, others related tales of difficulty keeping zinc in a protein. Suggested ways of overcoming the problem included: 1) Use of TCEP as a reducing agent 2)

[ccp4bb] post-doctoral or graduate student position

Post-doctoral or graduate student position available A post-doctoral position with competitive salary package (~US$40,000 + housing subsides, full healthcare coverage and up to 3 months bonus, tax is about 10%) is available at the laboratory of Shee-Mei Lok in the emerging infectious diseas

Re: [ccp4bb] CONECT records

Christina, phenix.elbow will generate the CONECT records for you. HTH Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Christina Bourne Sent: Thursday, October 02, 2008 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CONECT records

Re: [ccp4bb] Protein-DNA complex prepartion for crystallization

Just wandering, is your DNA dissolved in a buffered solution or just water? I would suggest to buffer your DNA solution prior mixing with the protein. Otherwise I guess that your pH in the protein-DNA mix is lower then the expected pH7.0 and maybe your protein does not like it. Cheers, Djordje >

[ccp4bb] CONECT records

Hello all, Probably a very basic question- where can I generate CONECT records in my pdb file for my ligand? Neither pdbset nor refmac did it for me. I am trying to run this file through ligplot, but the ligand is not being recognized. As compared to examples, a glaring difference is the la

[ccp4bb] postdoctoral or graduate student position, Singapore

A post-doctoral position with competitive salary package is available at the laboratory of Shee-Mei Lok in the emerging infectious disease program of the Duke-NUS. Duke-NUS graduate medical school situated in Singapore, is a global partnership between Duke University and the National Univer

Re: [ccp4bb] test data sets part II...

Hi Mark We are more than happy to help you setup a local repository - its fairly painless and cheap. Otherwise - we'll host your data - we have the solution worked out pretty much here and have moved on quite a bit from the Androulakis paper - see http://www.tardis.edu.au. It might cost yo

Re: [ccp4bb] test data sets part II...

Dear All, with regards to diffraction images storage (see also Androulakis et al., Acta Cryst. (2008). D64, 810–814: "Federated repositories of X- ray diffraction images"), I am all for it - one to be able to catch fraud, but more importantly so structures can be improved in the future and

Re: [ccp4bb] resuspending precipitated protein

hi Andy Here's my tip: If the protein is not denatured, but just precipitated, you can use the precipitate as research tool, trying to see if the protein will dissolve again with additives such as EDTA or divalent metal ions, or a bit of salt, or cofactor ATP or NAD, detergent etc (anything non

Re: [ccp4bb] SOme wquestions about refining.......

Fire up a recent version of coot and go through every step on the validation menu - but most im protantly the Ramachandran plot, the density fit analysis, unmodelled blobs, rotamer probabilities and finally and most importantly difference maps peaks. Then run molprobity (via the web site if yo

Re: [ccp4bb] R32 data

Hi Josiah, The primitive cell is what is important. The primitive cells for C2 and R32:H are the same as the P1 cell you report: (using phenix.explore_metric_symmetry) R32:H Niggli cell: (81.728198520053866, 81.728198520053866, 81.728198520053866, 84.166443879693517, 84.166443879693517, 84.166

Re: [ccp4bb] Protein-DNA complex prepartion for crystallization

Dilute both the Protein and DNA before mixing them at the molar ratio you require - I would aim to have the protein component at around 1 mg/ml. Mix, then concentrate together, till you reach the concentration you want. Antony. On Wed, Oct 1, 2008 at 6:52 PM, E rajakumar <[EMAIL PROTECTED]