Figure 3.

Quality of the Structure

(A) Representative fit of the AAV-DJ structure to the reconstruction of the fondaparinux complex. The density is contoured at 9 σ. (B) The occupancy-weighted difference map was calculated to best show the ligand-bound form of the viral protein (colored by atom type). The map at 5 Å resolution is shown at the 5 σ level. Density for the fondaparinux is noisier than in the conventional difference map (Figure 4A), as expected for non-unit difference coefficients. The bound protein structure is shown in green (backbone plus two arginines), whereas the unbound backbone is shown in red. Symmetry-equivalent subunits are colored purple.