Re: [ccp4bb] ligand occupancy

Hi Monica, Calculate the mean B-factor of all atoms that making interactions with each ligand in monomer A and B. Use those means values as B-factors for each ligand respectively. Adjust manually the occupancies, in order the B-factors for each ligand to stay after refinement close to

Re: [ccp4bb] occupancy of Metal

What is the mean B-factor of atoms that making interactions with each metal ion? Use those means values as B-factors for each Mg2+ ion respectively. Adjust manually the occupancies, in order the B-factors for each Mg2+ to stay after refinement close to the above values. George From:

Re: [ccp4bb] Assays for protein-ligand interaction?

Specifically for fluorescence does your ligand fluoresce? It is possible if it has indol group or some aromatic organic compound Does your protein has a tryptophan or tyrosines in the binding site? If yes may be a fluorescence titration experiment could be the solution. Also

Re: [ccp4bb] Isothermal titration calorimetry

: Colbert, Christopher [mailto:christopher.colb...@ndsu.edu] Sent: Saturday, March 23, 2013 5:56 PM To: George Kontopidis; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry George, would you please explain your comments? We've found the TA Instruments analysis software

Re: [ccp4bb] Isothermal titration calorimetry

Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23,

[ccp4bb] column tube

for a new column is more than 1500 €! Does anybody know if there is a company that could provide custom-made plastic tubing for chromatography columns? Thanks in advance for your answers, George Kontopidis Assοciate Professor of Biochemistry Veterinary School, University

Re: [ccp4bb] How to know if ADP exists in the ATP-binding site of bacterial expressed proteins

At 280nm absorbs Trp but Tyr and Phe (much less) as well. So your protein sample even without Trp will absorb. A mass spect experiment should show a presence of molecule with MW 507 (ATP) or MW 427 (ADP) George

Re: [ccp4bb] Kinase crystallization

if the ligand binding site is exposed to the solvent a bound ligand may help. if the protein has is flexible domains and ligand fix it in one conformation, a bound ligand will help even more. All the above assuming that the purity and the concentration of the protein are high. George

Re: [ccp4bb] Kd's in Crystals

--- George Kontopidis Associate Professor of Biochemistry Head of Biochemistry Veterinary School, University of Thessaly Trikalon 224, Karditsa 43100, Greece Tel: +30 24410 66017 Mob: 69 342 643 75 Fax: +30 24410 66041 e-mail: gkontopi...@vet.uth.gr

Re: [ccp4bb] Putting ligand in the protein structure

You need protein structure, a different e. density map (1Fo-1Fc) and your ligand structure. Then from COOT menu select Other Modelling Tools and click Find Ligand. You can also move manually the ligand into the density map. George -Original Message- From: CCP4 bulletin board