Yes in the first couple of rounds of refinement it refines very well for a 3.2 angstrom structure (Now at 30%/24% Rfree/R). Everything Packs contiguously except for a "donut" hole in between six dimers that are related by symmetry. Trying to put a molecule there disrupts the symmetry and leads to clashes. I have a synchrotron trip next week, hopefully this should help clear things up a bit.
On Wed, Mar 19, 2014 at 12:17 AM, Eleanor Dodson <[email protected]>wrote: > I think you have solved it! That is an excellent LLG and if you can't see > anything else in the map, then there s prob. not another molecule. > Does it refine? If you look at the maps following refinement any missing > features should become more obvious. > Solvent content of 65% is not uncommon. > Eleanor > > > On 19 Mar 2014, at 03:46, Yarrow Madrona wrote: > > Hello CCP4 Users, > > I recently collected data in-house on an Raxis IV and am trying to solve a > 3.2 angstrom structure. > > I have obtained only "partial solutions" using Phaser and would like some > help. I believe I only have two molecules in the ASU instead of three as > suggested by the mathew's calculation. I believe I have two molecules in > the ASU with a space group of P312 despite a high solvent content. I have > outlined by line of reasoning below. > > 1. Indexes as primitive hexagonal > > 2. Self rotation function (MolRep) gives six peaks for chi = 180. (I'm > assuming chi is equivalent to kappa for Molrep) supporting the 2 fold axis > in the P312 space group. See this link, > https://www.dropbox.com/s/sj7c28pvuz7fei2/031414_21_rf.pdf > > 3. Scaling in P3 gives 6 molecules/ASU predicted by Mathew's calculation. > Phaser gives solutions for only 4 molecules. > > 4. Scaling in P312 gives 3 molecules/ASU predicted by Mathew's > calculation. Phaser gives solutions for only 2 molecules. > > Mathews calculation for data scaled in P312: > > *For estimated molecular weight 44000.* > > *Nmol/asym Matthews Coeff %solvent P(3.20) P(tot)* > > *____________________________________________________________* > > * 1 6.84 82.03 0.00 0.00* > > * 2 3.42 64.07 0.18 0.13* > > * 3 2.28 46.10 0.81 0.86* > > * 4 1.71 28.13 0.01 0.01* > > * 5 1.37 10.17 0.00 0.00* > > *____________________________________________________________* > > *Phaser Stats:* > > Partial Solution for data scaled in P312: > > RFZ=11.7 TFZ=27.4 PAK=0 LLG=528 TFZ==18.8 RF++ TFZ=52.1 PAK=0 LLG=2374 > TFZ==30.3 > > 6. No peaks in patterson map (No translational symmetry). > > 5. Very strong 2fo-fc density for two ligands in each monomer (Heme and 4 > bromo-phenyl Immidazole) despite not including them in the search model. > > 6. There is only one "black hole" where it would be possible place another > subunit but there is not much interpretable density and the symmetry of the > space group would be broken if this was done. Six Dimers are arranged > around this hole. I can post a picture if anyone wants to see it. > > 6. Early refinement of the "partial solution" gives an Rwork/Rfee ~ > 24%/31% for a 3.2 angstrom data set. Probably over parameterized judging by > the gap in R/Rfree but still better than I would guess if I had only 2/3 of > the ASU composition. > > *My belief is that there really is only two molecules in the ASU and that > there just happens to be a very large solvent channel giving a 65% solvent > content.* > > *I would like help in determining whether this is likely or if I have > missed something. Thank you for your help in advance!* > > *-Yarrow* > > > Post Doctoral Scholar > > UCSF > > Genentech Hall, Rm N551 > > 600 16th St., San Francisco, CA 94158-2517 > > >
