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
>>
>
>
>