Hi Savvas, Native PAGE and DLS suggest a monodisperse monomer in solution.
On Wed, Mar 19, 2014 at 12:12 PM, Savvas Savvides <savvas.savvi...@ugent.be>wrote: > Dear Yarrow > your toroidal structure suggests that the protein may actually have the > propensity to assemble as such in solution, hinting a connection to a > biologically relevant state. Do you have any experimental information that > it does so? e.g. via SAXS, MALS, native PAGE etc.? > > best regards > Savvas > > ---- > Savvas Savvides > Unit for Structural Biology, L-ProBE > Ghent University > K.L. Ledeganckstraat 35, 9000 Ghent, Belgium > Tel/SMS/texting +32 (0)472 928 519 > Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html > > > > On 19 Mar 2014, at 16:58, Yarrow Madrona <amadr...@uci.edu> 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> 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> 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 >>> >>> >>> >> > >
