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 > **********************************************************************
