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Yes, thats correct. I didn't show it but the donuts move in the direction perpendicular to the paper. On Wed, Mar 19, 2014 at 12:07 PM, Felix Frolow <[log in to unmask]>wrote: > Very reasonable structure, I guess in the direction perpendicular to your > picture you will have next donut etc. > You can call this - nan-pore ;-) > Dr Felix Frolow > Professor of Structural Biology and Biotechnology, Department of > Molecular Microbiology and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica F, co-editor > > e-mail: [log in to unmask] > Tel: ++972-3640-8723 > Fax: ++972-3640-9407 > Cellular: 0547 459 608 > > On Mar 19, 2014, at 18:37 , Eleanor Dodson <[log in to unmask]> > wrote: > > How pretty - I love circular molecules! > Eleanor > > > On 19 March 2014 15:58, Yarrow Madrona <[log in to unmask]> 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]> 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]> 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 >>>> >>>> >>>> >>> >> > >