Crystallographic refinement of the structure of actinidin at 1.7 Å resolution by fast Fourier least-squares methods

The structure of the proteolytic enzyme, actinidin, has been refined by fast Fourier least-squares methods [Agarwal (1978), Acta Cryst. A34, 791-809]. Atomic positions were refined independently by the least-squares program, with the whole protein structure being regularized at intervals. After an initial refinement phase with an overall temperature factor, B, only, individual isotropic B values for all atoms were also refined. Overall, the crystallographic R factor was reduced from 0.429 (for 14 800 reflections to 2.0 Å resolution) to 0.171 (for all 23 990 reflections between 10 and 1.7 Å resolution), with a final estimated accuracy in atomic positions of <0.1 Å. The final model comprises 1657 protein atoms, constrained close to standard geometry, and 163 solvent molecules, the latter identified using somewhat selective criteria. Most of the structure refined automatically with an average shift of 0.45 Å for main-chain atoms and 0.56 Å for side-chain atoms (maximum shift about 1.5 Å). Some larger shifts resulted from manual intervention. Groups of atoms with high B values, or which were not refining well, were removed at intervals for scrutiny in difference maps, and major corrections were made to the conformations of 16 side chains and two peptide units. One correction to the amino-acid sequence was made (Asp 86 → Glx 86) and disordered conformations were introduced for five side chains. The whole refinement was completed in three months.