Errors and reproducibility in electron-density map interpretation

Three investigators, with varying levels of experience, independently built and refined the structure of Escherichia coli ribokinase at 2.6 Angstrom resolution. At the end of the refinement/rebuilding processes the models had essentially converged, although each had its own particular pattern of remaining errors. The subsequent refinement of the same structure at 1.8 Angstrom resolution allowed an overall quality check of each of the lower resolution models, and an analysis of which graphics-based tools were generally most efficient in locating these errors. Criteria which are useful in the application of Ramachandran, main-chain and side-chain database and real-space fit analyses are presented.