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 th

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: CCP

Re: [ccp4bb] density near Histidine

Rotate chi2 bond (CB-CG) and have two alternative conformations for the His. Add two water molecules (50% occupancy) each making a H-bond with the NE2 atoms (alternative 1 and 2) of the His. George From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of SD Y Sent: Saturda

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 fluorescence

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 sof

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, 20

[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 of

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] Substrate(water insoluble) Soaking

Take one crystal and put it in mother liquor. Increase gradually (in two separately experiments) your ethanol and DMSO concentration (in my experience it could go up to 10%v/v after 1 week for some crystals) in order to find out the concentration that your crystal can stand without dissolve or crac

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 [mailto:[EM