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, <herman.schreu...@sanofi.com> 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Bjørn Panyella Pedersen > Gesendet: Dienstag, 3. Juni 2014 21:01 > An: CCP4BB@JISCMAIL.AC.UK > 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 >
