I have used CNS before, but not for this sort of refinement. I see in the bindividual.inp file that I can "select atoms to be included"--it is defaulted at "known and not hydrogen". Do you know the proper nomenclature for selecting a Zn ion in chains A and B?
Thanks, Chris On 5/6/14, Steven Herron <[email protected]> wrote: > > Refining the occupancy will help your R-factor and flatten your density, > but you need to be careful to also refine the B-factor of the metal > ion. Don't refine both the occupancy and the B-factor during the same > run (the two are correlated at this resolution), refine the occupancy of > just the metal ion and then refine the B-factor of just the metal ion > (repeat as needed). I used X-plor/CNS to do my refinements, so it was > easy to refine the occupancy (or B-factor) of just the metal ion. After > a few rounds of refinement both parameters will stop changing and you > will have your answer. The final B-factor of the metal ion should be > similar to the amino acid residues that are coordinated to it. > > Soaking in several different ion concentrations and collecting > additional datasets is also a good idea (if you have the time). I did > this type of experiment once before (see: JBC 278(14):12271-7. [ Apr 4, > 2003]) (or: http://www.ncbi.nlm.nih.gov/pubmed/12540845). I soaked in > several different Ca2+ ion concentrations and was able to determine the > binding affinity for that calcium ion using crystallography. > > To make sure I was not stuck in a local minima, I would modify either > the occupancy of the B-factor of the metal while keeping the other fixed > and do a refinement. I even tried both large and small changes (both > increases and decreases in value). It always came back to the earlier > answer. > > Different Ca2+ ion concentrations can give some additional insight into > the metal binding site. Between the no-Ca2+ structure and the high-Ca2+ > structure there was a conserved Asp-residue that changed conformation. > So, I soaked in the appropriate amount of Ca2+ to see the residue in > both positions. There was a high correlation between the asp residue > orientation and the Ca2+ ion occupancy. > > Steven Herron > [email protected] > > > > > On 5/6/2014 11:02 AM, Chris Fage wrote: >> Hi Everyone, >> >> In my 2.5-angstrom structure, there is negative Fo-Fc density >> surrounding a metal ion after refining in Phenix. From anomalous >> diffraction I am certain of the metal's identity and position in each >> monomer. Also, the ion is appropriately coordinated by nearby side >> chains. Should I be refining the occupancy of the ion in attempt to >> "flatten" the negative density? I am considering soaking the metal ion >> into crystals or cocrystallizing and collecting additional datasets. >> >> Thanks for your help! >> >> Regards, >> Chris > >
