I have heard "hard" and "soft" many times now about O's and N's--to what property of those ligands does this metaphor refer?
JPK On Thu, Feb 24, 2011 at 12:47 PM, Jeffrey D Brodin <jbro...@ucsd.edu> wrote: > Alex, > > I modeled in the bis-tris with the tertiary amine and and his imidazole > coordinating axially and the four oxygens coordinating in the equatorial > plane. However, it's hard for me to tell from your images if there are two > His coordinating? Either way, that crescent shape could easily be explained > by a bis-tris molecule, you'll just have to figure out how exactly to model > it in. It's also possible that the metal is a Mg, but as people have already > mentioned, nitrogens probably wouldn't coordinate very tightly to a hard > metal. Lastly, I'm also not sure off the top of my head how tightly bis-tris > binds metals, but it should be an easy number to look up. Hope this helps, > > Jeff > On Feb 24, 2011, at 9:02 AM, Alex Singer wrote: > >> Hi -- thank you for all your help. The majority opinion seems to be a >> metal for the sphere (Ni from the Ni-affinity column, which (Joe >> Patel, correct) was used during purification, but Zn and Fe were also >> mentioned), and either water molecules, bis-tris or some other small >> molecule forming the crescent. Just looking at the density, the >> occupancy would seem to be quite high, so I'm surprised that a Ni ion >> (or a contaminating metal ion) could have gone through the >> purification and still remained at high enough concentration to be >> clearly visible in the crystals. However, I'll still try this but >> first some points of clarification and questions which you can either >> email me seperately or post to the the group. >> >> a. it was collected at beamline 19-BM at Argonne, so radiation damage >> is an issue. Thierry Fishmann -- for the gln residue, there was >> difference density for the gamma carbon after the first conformation >> was modeled in, thus the addition of the second conformation, which I >> agree is suspect. What does the radiation damage do chemically and >> would that make the gamma carbon more mobile? >> >> b. Jeffrey D Brodin -- how did you model in the bis-tris? Looking at >> the bis-tris molecule from Hic-up, was the N at the centre of the >> crescent and the O6 and O8 at the edges? >> >> c. JR Helliwell -- there are 4 molecules in the AU, but two H138's >> are pointing into the solvent. Thus the molar ratio of protein >> molecules to "thing 1" is 4:1. Also looking at the images, I see no >> ice rings -- the images look pretty good. Can you tell me more about >> the series termination effects? >> >> Again thank you for your help and I'll let the group know how it worked >> out. >> >> Alex >> >> -- >> Dr. Alex Singer >> C.H. Best Institute >> 112 College St. Room 70 >> University of Toronto >> Toronto, Canada, M5G 1L6 >> 416-978-4033 > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
