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Hi Yarrow, That solution looks very reasonable to me. If you are worried about the size of your doughnut-hole, look at the packing of the latest structure we solved. :) https://dl.dropboxusercontent.com/u/5116503/4J05.png best -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 03/19/2014 08:58 AM, Yarrow Madrona wrote: > Thank you to everyone for their input. I am posting a picture to some of > the symmetry related molecules shortly. There are six dimers related by > symmetry (60 degrees) with a "donut" hole in the middle. This was > troubling to me as I have solved mostly tighter packing structures > (monoclinic or orthorhombic) in the past. If expanded further there are > a bunch of tightly packed donut holes (though I didn't show these). > > I want to know if this is really a viable solution. The crystals are > huge (300microns X 300microns) and this would maybe explain why they are > only diffracting to 3.2 angstroms. Thank you! > > https://www.dropbox.com/s/r01u37owbkz9pon/donut.png > > -Yarrow > > > On Wed, Mar 19, 2014 at 6:59 AM, Yarrow Madrona <[log in to unmask] > <mailto:[log in to unmask]>> wrote: > > 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 > <[log in to unmask] <mailto:[log in to unmask]>> 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 >> > > >