Structure determination of adeno-associated virus 2: Three complete virus particles per asymmetric unit

The atomic structure of adeno-associated virus 2 (AAV-2) has been determined to 3.0 Å resolution. AAV-2 crystallized in space group P1, with unit-cell parameters a = 249.7, b = 249.7, c = 644.8 Å, α = 90.0, β = 101.2, γ = 120.0°. The crystals contained three full virus particles in the asymmetric unit, allowing 180-fold non-crystallographic symmetry averaging. The particle orientations were determined using the self-rotation function and found to have similar but resolvably different orientations. Approximate alignment of icosahedral and interparticle threefold screw symmetry led to a native Patterson that was interpretable in terms of approximate particle positions. Accurate positions required a Patterson correlation search that was constrained to be consistent with non-crystallographic threefold projection symmetry evident in the diffraction intensities. Initial phases to 15.0 Å resolution were calculated by molecular replacement using the known structure of a distantly related homolog (23% sequence identity). Real-space averaging was performed and phases were extended from 15.0 to 3.0 Å. An atomic model was fitted and refined using a simulated-annealing real-space procedure.