Dear Jacob For a review of this topic see http://www.tandfonline.com/doi/full/10.1080/08893110310001643551#.UyCVLikgGc0
I also refer you to the more recent OUP IUCr book Chayen, Helliwell and Snell ie which includes these topics:- http://global.oup.com/academic/product/macromolecular-crystallization-and-crystal-perfection-9780199213252;jsessionid=5564F908743CCE57BAD506586B47B6CC?cc=gb&lang=en&; I declare a 'perceived conflict of interest' in making this book suggestion to you. Best wishes John Prof John R Helliwell DSc > On 12 Mar 2014, at 16:59, "Keller, Jacob" <kell...@janelia.hhmi.org> wrote: > > Not sure I understand why having statistical disorder makes for streaks--does > the crystal then have a whole range of unit cell constants, with the spot at > the most prevalent value, and the streaks are the "tails" of the > distribution? If so, doesn't having the streak imply a really wide range of > constants? And how would this be different from mosaicity? My guess is that > this is not the right picture, and this is indeed roughly what mosaicity is. > > Alternatively, perhaps the streaks are interpreted as the result of a duality > between the "unit cell," which yields spots, and a "super cell" which is so > large that it yields extremely close "spots" which are indistinguishable from > lines/streaks. Usually this potential super cell is squelched by destructive > interference due to each component unit cell being very nearly identical, but > here the destructive interference doesn't happen because each component unit > cell differs quite a bit from its fellows. > > And I guess in the latter case the "supercell" would have its cell constant > (in the direction of the streaks) equal to (or a function of) the coherence > length of the incident radiation? > > I know some attempts have been (successfully) made to use diffuse scattering, > but has anyone used the streak intensities to determine interesting features > of the crystallized protein? > > JPK > > > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew > Leslie > Sent: Wednesday, March 12, 2014 12:25 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] twinning problem ? > > Dear Stephen, > > I have seen a similar effect in the structure of > F1-ATPase complexed with the full length inhibitor protein. The inhibitor is > a dimer, and it actually couples 2 copies of the ATPase, but it crystallised > with only one copy of the ATPase per asymmetric unit. When I solved the > structure by MR, I saw additional density that could not be accounted for. > The extra density was, in fact, a second ATPase molecule that was related to > the first by a 120 degree rotation about the pseudo 3-fold axis of the > enzyme. The "dimers" were packing with statistical disorder in the crystal > lattice. This gave rise to clear streaking between Bragg spots in the > diffraction images in a direction that was consistent with that expected from > the statistical packing of the inhibitor linked dimers. > > Two copies of F1 were included in the refinement, each with occupancy 0.5. > the final Rfree was 27.7% (2.8A data). Prior to introduction of the second > copy of F1, the Rfree was 37%. > > More details are in Cabezon et al., NSMB 10, 744-750, 2003 > > Best wishes, > > Andrew > > > >> On 11 Mar 2014, at 14:04, Stephen Cusack <cus...@embl.fr> wrote: >> >> Dear All, >> I have 2.6 A data and unambiguous molecular replacement solution >> for two copies/asymmetric unit of a 80 K protein for a crystal integrated in >> P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9. >> Refinement allowed rebuilding/completion of the model in the noraml >> way but the R-free does not go below 30%. The map in the model regions looks >> generally fine but there is a lot of extra positive density in the solvent >> regions (some of it looking like weak density for helices and strands) and >> unexpected positive peaks within the model region. >> Careful inspection allowed manual positioning of a completely different, >> overlapping solution for the dimer which fits the extra density perfectly. >> The two incompatible solutions are related by a 2-fold axis parallel to a. >> This clearly suggests some kind of twinning. However twinning analysis >> programmes (e.g. Phenix-Xtriage), while suggesting the potentiality of >> pseudo-merohedral twinning (-h, l, k) do not reveal any significant >> twinning fraction and proclaim the data likely to be untwinned. (NB. >> The programmes do however highlight a non-crystallographic translation and >> there are systematic intensity differences in the data). Refinement, >> including this twinning law made no difference since the estimated twinning >> fraction was 0.02. Yet the extra density is clearly there and I know exactly >> the real-space transformation between the two packing solutions. >> How can I best take into account this alternative solution (occupancy seems >> to be around 20-30%) in the refinement ? >> thanks for your suggestions >> Stephen >> >> -- >> >> ********************************************************************** >> Dr. Stephen Cusack, >> Head of Grenoble Outstation of EMBL >> Group leader in structural biology of protein-RNA complexes and viral >> proteins Joint appointment in EMBL Genome Biology Programme Director >> of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell >> Interactions (UVHCI) >> ********************************************************************** >> >> Email: cus...@embl.fr >> Website: http://www.embl.fr >> Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 >> Fax: (33) 4 76 20 7199 >> Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, >> 38042 Grenoble Cedex 9, France >> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, >> 6 Rue Jules Horowitz, 38042 Grenoble, France >> **********************************************************************
