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 <[email protected]> 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 < > [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 >> >> >> >
