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It helps to look at the output from the  truncate step quite critically.
First is there a non cryst translation of 1/2,1/2,1/2 indicated in the P4 2i2 data set?

If so then the I centring at lower resolution might just be approximate..

If there is NC translation then other twinning statistics are distorted and I find the only semi-reliable one is the L test.

But if you say there is no room for your protein with that translation and 4/mmm symmetry then there must be twinning or you have crystallised something else!

Eleanor


On 4 June 2014 08:48, <[log in to unmask]> wrote:
Dear Bjørn,
I guess the first step to enlightment is to recognize that we as mere mortals are not able to deduce the space group from diffraction data alone. All Aimless, XDS etc. can produce are educated guesses what the space group might be. Especially when twinning is involved, the crystal packing may not heed the rules and classifications that we humans try to impose. In many cases, one might have to go down to P1 and solve the structure in P1 to find out what the true space group is.

Here are some comments to your questions:
-the same protein under the same crystallization conditions and even in the same drop may produce crystals with very different crystal packings, even with the same unit cell, so your 4 and 7.5Å crystals may be different.
-If there is no way to fit the protein in the asymmetric unit that is a very strong indication that you do have twinning.
-There have been some discussions in the CCP4BB, but I do not believe that twinning can generate body centering.
-You might be barking at the wrong tree and the twinning axis might be parallel to the 4-fold axis, or even generating the 4-fold. You may even have 4-fold twinning.
-You may have pseudo body centering, which is perfect at low resolution, but breaks down at higher resolution. As a test, you could process your 4Å data only to 7.5Å and see what the statistics would look like.

What I would do:
If you have more crystals, collect data on them all, maybe there is one which is not or not perfectly twinned.
If there is a model which could be used for molecular replacement: process the data in P4, I4, P222 and P1 and run molecular replacement with all possible space groups for both crystals.

However, at 4Å with unclear twinning, solving your structure will be tough.

Best,
Herman


-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Bjørn Panyella Pedersen
Gesendet: Dienstag, 3. Juni 2014 21:01
An: [log in to unmask]
Betreff: [ccp4bb] possible twinning issue in P4212 / I422

Dear All,
I have a strange potential twinning issue that I cannot understand. I've searched high and low on all the internets to find an answer but have come up empty-handed, so I look to the wisdom of The Board to enlighten me.

I have a 4'ish Å dataset that processes nicely in P 4 21 2 (#90).
However intensity distributions indicate possible almost perfect twinning (eg. <I^2>/<I>^2 : 1.592 ). So I speculate that the real space group might be P 4 (#75).

Recently we collected a new fairly low resolution (7.5Å) dataset, from the same type of crystals (same purification, same conditions).
But the space group in XDS and aimless now comes out very clearly as either I422 (#97) or I4212 (#98) (screw-axis is unclear given the data).
The unit-cell parameters are exactly the same as in sg #90, which btw.
means that in the body-centered lattice there is no way the protein can fit in the asym. unit.

So I guess what I don't understand is: Is it possible to go from a primitive lattice to a body-centered lattice by twinning. Is this just a low-resolution artifact? Or is this a P4 unitcell that can appear like
P4212 or I422 depending on small variations (weak dehydration or similar).

Has anyone experienced something similar? Am I missing a basic facet of how twinning works, or is something else at play here?

Thanks for any insights or suggestions!

All the best,
/Bjørn

--
Bjørn Panyella Pedersen
Macromolecular Structure Group
University of California, San Francisco