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