Re: [ccp4bb] peptide fragment

2012-07-19 Thread John Hinks
Hi Leonard, I would treat this like a MS/MS ion search experiment looking for the peptide via MASCOT or similar. Talk to some local Mass Spec people, I'm certain they could identify it and then you'd be closer to an explanation. John. Dr. John Hinks Syngenta Jealott's Hil

Re: [ccp4bb] How to optimize protein-DNA complex conditions?

2010-09-13 Thread John Hinks
Hi Yang. Adding to what Phoebe has said below, remember that when running polyacrylamide shift gels using TBE and in the absence of SDS, your protein (depending on its charge) may not migrate into the gel, or may in fact migrate out of the well altogether (in the absence of DNA binding). In or

Re: [ccp4bb] Problems in purification

2010-09-13 Thread John Hinks
Hi Ganesh, two things I'd advise that might make a difference for you: 1. Improved media for better expression See "Protein production by auto-induction in high-density shaking cultures" by W.F. Studier Protein Expression and Purification 41 (2005) 207-234 (there's also a re

Re: [ccp4bb] Suggestions for Reducing Protein Precipitation

2010-08-13 Thread John Hinks
Hi Matt, if you have a crystallisation robot (and if you haven't you can still do this manually) you can use a simple microbatch under oil experiment to determine the likely optimum pH and salt concentration. Just set up a grid across pH (I usually use a phosphate buffer for this as it is easi