Electron density server at Uppsala university

Electron density server at Uppsala university provides access to calculated electron-density maps and evaluates the fit between PDB models and experimental crystallographic data to assess model quality.

Key Features:

• Electron-density map access: Provides calculated electron-density maps for approximately 87% of PDB entries that have associated structure factors and where map calculations reproduce the published R value within a five percentage point margin.
• Map calculation from structure factors: Calculates electron-density maps using the associated structure factor amplitudes.
• Model fit assessment: Compares calculated electron density to deposited crystallographic models to evaluate how well models correspond to experimental data.
• Goodness-of-fit statistics and plots: Generates statistics and plots that quantify agreement between structural models and experimental electron density.
• Robust map-generation handling: Addresses challenges encountered during map generation to ensure robustness of the produced maps and analyses.

Scientific Applications:

• Model quality assessment: Evaluating the accuracy and reliability of PDB structural models by direct comparison to experimental electron density.
• Structural biology research: Supporting interpretation and validation of protein structures and their properties using electron-density analysis.
• Quantitative model validation: Providing quantitative measures and plots for assessing model-to-data agreement across crystallographic entries.

Methodology:

Calculates electron-density maps from structure factor amplitudes for PDB entries, compares the reproduced R value to the published R (within a five percentage point margin), and generates statistics and plots quantifying model-to-density agreement.