Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution

The previously reported structural model of porcine pancreatic alpha-amylase has been corrected and improved by a genuinely independent structure solution. The electron density map was established by multiple isomorphous replacement (m.i.r.; using 5 derivatives) and subsequent solvent-flattening at 2.8 A resolution. The sequence was built into the well-defined regions of the m.i.r. map; this partial model was refined using a simulated annealing refinement method with phase restraints. Phase combination of m.i.r. phases and phases of the partial model allowed the completion of the model. The final refinement was based on 29,838 independent reflections in the 8 to 2.1 A resolution range. A final R-factor of 15.6% was obtained with a model obeying standard geometry within 0.014 A in bond lengths and 2.8 degrees in bond angles. The final model consists of all 496 amino acid residues, 1 calcium ion, 1 chloride ion and 353 water molecules. The model is described in detail; the calcium and chloride binding sites are characterized.