Sfcheck

Sfcheck evaluates structure-factor data from X-ray diffraction experiments and quantifies agreement between experimental structure-factor amplitudes and atomic coordinates.

Key Features:

• Automatic evaluation: Performs automated analyses using structure-factor amplitudes and atomic coordinates as inputs.
• PostScript pictorial output: Produces concise PostScript graphics resembling outputs from PROCHECK (Laskowski et al., 1993) for visual inspection.
• Data completeness assessment: Evaluates the completeness of the supplied structure-factor data.
• Structure-factor uncertainty and optical resolution: Assesses structure-factor uncertainty and optical resolution using information from the Patterson origin peak.
• Resolution dependence (d spacing): Analyzes how parameters vary as a function of nominal resolution (d spacing).
• Global agreement metrics: Recomputes R factor, the correlation coefficient between observed and calculated structure-factor amplitudes, and Rfree when applicable, and provides several estimates of average error in atomic coordinates.
• Local agreement assessment: Evaluates per-residue agreement for macromolecule backbone and side-chain atoms, solvent atoms, and heterogroups using normalized average atomic displacement, local density correlation coefficient, and polymer chain connectivity, with support for the omit-map procedure.

Scientific Applications:

• Refinement monitoring: Tracks agreement between experimental data and models during structure refinement to monitor refinement procedures.
• Structure validation of deposits: Assesses deposited structures in databases to verify their quality and reliability.
• Model validation for structural interpretation: Provides global and local assessments to support rigorous validation of structural models for molecular structure–function studies.

Methodology:

Uses structure-factor amplitudes and atomic coordinates as inputs; generates PostScript pictorial outputs; evaluates data completeness; assesses structure-factor uncertainty and optical resolution from the Patterson origin peak; analyzes parameter dependence on nominal resolution (d spacing); recomputes R factor, correlation coefficient between observed and calculated structure-factor amplitudes, and Rfree; estimates average error in atomic coordinates; performs per-residue assessments using normalized average atomic displacement, local density correlation coefficient, and polymer chain connectivity, with optional omit-map computations.