Re: [ccp4bb] offtopic: effect of compound impurities on ITC?

2010-08-26 Thread Justin Hall
Hi Francis, I might save you some time by telling you up front you should just go back and purify your compound to remove the impurity, you dont even need to read the rest of this, just go. Along the lines of what Savvas was saying, with any equilibrium binding assay between two direct

Re: [ccp4bb] relationship between B factors and Koff

2010-11-19 Thread Justin Hall
Hi Sebastiano, I have had some experience with protein:protein complexes with KD ~ 10-1 uM, kinetic characterization and trying to purify a complex of these proteins using SEC. While I would say that if you have reliable evidence from SPR that you have a fast on (high Kon), then you must

Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread Justin Hall
Hi Liu, If I understand your question correctly, youre asking how different do two structures need to be for one to be new'. If by new you mean a new fold, then the answer is NO. Your structure and the homolog have the same fold. However, if your structure is the first structure of a

[ccp4bb] A tool for MR that renumbers and replaces amino acids of your search model

2011-02-03 Thread Justin Hall
Dear Community, I am looking for a tool that can convert a potential MR search model to match the residue number and a.a. type of my actual protein. Specifically, I have a homolog structure, with slightly different start and stop residues, and several non identical a.a.s relative to my

[ccp4bb] off topic: GPCR membane insertion/orientation

2011-03-04 Thread Justin Hall
Dear Community, In trying to trouble shoot an experiment I have become interested in the cellular process that regulates the insertion and proper orientation of membrane proteins. I am looking for references for how a GPCR is correctly oriented during expression (i.e. the extra cellular

Re: [ccp4bb] protein lost activity after size exclusion chromatography

2011-03-16 Thread Justin Hall
Hi Harvey, Well, knowing nothing about your protein, allow me to ruminate anyway... It sounds like you are exploring the possibility of a metal ion or other cofactor being lost. This is a reasonable first thing to check, but your buffer exchange steps should allow small cofactors (smaller

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

2011-06-16 Thread Justin Hall
Hi Alex, I read Filip's comment about volume not as a path length argument, but about concentration uncertainty in mixing small volumes to dilute a sample down before measuring it (?). I have never had to make a dilution for my nanodrop (my proteins are usually not that concentrated),

[ccp4bb] A new historical structural achievement

2011-07-21 Thread Justin Hall
Dear CCP4BB, Forgive me for soap boxing, but yesterday the first structure of a GPCR/Gprotein complex was released (PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=3SN6, article: http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature10361.html). Recently a student

[ccp4bb] anisotropic diffraction in refinement

2009-09-01 Thread Justin Hall
? Cheers~ ~Justin Hall Oregon State University

[ccp4bb] Summary for Anisotropic Diffraction In Refinement question

2009-09-15 Thread Justin Hall
Dear All; In response to my Anisotropic Diffraction In Refinement, which asked for suggestions for how best to proceed with refinement with an anisotropic data set, I received a large number of responses which overwhelmingly suggested using the UCLA Anisotropy Server

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Justin Hall
Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Justin Hall
Thanks to everyone for the info on Zalman monitors, sorry to have muddied the waters for you Ajit. Best wishes~ ~Justin Quoting Justin Hall hallj...@onid.orst.edu: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD