Hi Bjorn, Thanks for your example. Those are some big gaps to be sure.
On Wed, Mar 19, 2014 at 1:38 PM, Bjørn Panyella Pedersen <bj...@msg.ucsf.edu > wrote: > 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 <amadr...@uci.edu >> <mailto:amadr...@uci.edu>> 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 >> <eleanor.dod...@york.ac.uk <mailto:eleanor.dod...@york.ac.uk>> 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 >>> >>> >> >> >> > > >
