Re: [ccp4bb] "inclusion body"

Lower temperature, use chaperones (e.g. TAKARA set), refolding? Quoting shivesh kumar <[EMAIL PROTECTED]>: Dear all, Sorry for the off-topic question... What can be done to avoid a protein going inside inclusion body.The gene is cloned in pET30a with C-ter his tag and expressed in BL21-DE3 fr

[ccp4bb] Compound behaviour/vulnerability/truncation software/server

Dear all, I was wondering if anyone knew of any software or server that could predict possible points of specific venerability to physical or chemical stresses/attack, which may lead to likely truncation of a given compound? Another possibility would be software that would take a compound as an

Re: [ccp4bb] Thermofluor experiment

Hi, I am interested in using the thermofluor to assess the stability of my protein in different buffers. Can anyone recommend a vendor that supplies buffer screens, possibly in 96 well format? Not crystallization buffers, just ordinary storage buffers. Thanks brenda Quoting Andreas Förster

Re: [ccp4bb] finicky protein

Did you filter your lysate through .45 then .22 filters? cheers b Quoting James Stroud <[EMAIL PROTECTED]>: Try refolding before purification. On Mar 2, 2008, at 11:47 PM, Tim Gruene wrote: Hi all sorry, for offtopic query... I am trying to purify my protein by Ni-NTA affinity chromato

[ccp4bb] torsion restraints COOT

Dear all I am doing molecular replacement with a model of sequence identity 42%. Have been trying numerous combinations of weighting in refmac of CCP4. However the geometry of the model is not being maintained. I am then trying manual fitting of the model in COOT. However when torsion restraints a

[ccp4bb] Cocrystals - should they pop up under native conditions?

Hello all, I am expecting a somewhat homogeneous reply to this one, but that is fine and welcomed as are anecdotal experiences. I am running co crystallisation experiments and have thus far been trying under oil screens with some success (i.e. various hits in various conditions resulting in cryst

[ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I ha

Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?

POSA at the Godzik lab does exactly what you are after, flexibly! http://fatcat.burnham.org/POSA/ Hi all=A3=AC I want to produce structure-based multiple sequence alignment of my =20= protein with five of its homologs on DALI server. However, when I =20 tried the "Database Search Form", on

[ccp4bb] I have my bound ligand (I think), now what?

Hello all, right, I think I have found a ligand bound to my protein. I used the COOT utility to find the ligands after reading in a model and library file generated by sketcher of my ligand. Now I am a bit unsure as to how to proceed? How can I 'accept' a state and/or refine it? Maybe there

Re: [ccp4bb] how to change a membrane protein into a water soluble protein?

Another option is refolding which can increase soluble protein content and is used routinely to achieve soluble protein such as the TIMPs http://peds.oxfordjournals.org/cgi/content/abstract/7/8/1035 http://www.proteinscience.org/cgi/reprint/11/10/2493.pdf?ck=nck that said, this is not true of

[ccp4bb] Import and merge data collected from TWO sources?

Is this possible? Currently I have two crystal data's. I have been importing the scaled averaged files using d*trek. The only difference between the two crystals is that one has been soaked with a ligand. Now I want to see if it is there. Is there a way to import both sets of data at the same