SAXS data analysis and rigid body modeling.
(A) The experimental SAXS profile of recombinant Endo338, measured at the ID14-3 BioSAXS beamline. The Kratky plot (inserted), displays a gaussian behavior, which indicates the well folded nature of the construct. (B) The distance distribution function, p(r) obtained from GNOM with a Dmax of 9.4 nm also suggests a compact structure. (C) The orphan domain model obtained from I-TASSER together with 5 Man5NAG2 glycans, restricted by their attachment sites was fitted by rigid body modeling with SASREF, yielding a fit of the model (red line) against the experimental Endo338 scattering profile (blue crosses) of χ2 = 1.1. The input models used, are depicted above the fit curve. (D) The resulting model is displayed as a cartoon in three orthogonal views, with the attached sugars depicted as balls, fitted into the molecular envelope from DAMMIF.