Building 3-D structures from Electron Density Maps

A) OBJECTIVES

  • Build an atomic model of a protein into your experimental electron density map.
  • Learn how to recognize density features (helices, sheets, chain direction, sidechain shapes)
  • Learn how to position poly-ALA helices into density
  • Learn how to recognize and mutate residues to fit the density

    B) ACTIVITIES:

  • Placing Alpha helices and beta strands in density.
  • Assigning protein sequence to density
  • Improve fitting by real space refinement prok_Fp_phases_dm2012.mtz

    C) COOT: LOADING EXPERIMENTAL STRUCTURE FACTORS AND PHASES TO MAKE THE ELECTRON DENSITY MAP .

    Download the MTZ file to calculate the electron density map in COOT
    1. Open COOT
    2. LOAD MTZ FILE: In the FILE TAB --> OPEN MTZ, MMCIF: Load prok_Fp_phases.mtz , CHECK Use Weights and OK
    3. Calculate Skeleton of the MAP: Open DISPLAY MANAGER--> PROPERTIES of MAP 0 --> SKELETON
    4. Place Helix: In the CALCULATE tab--> OTHER MODELING TOOLS --> PLACE HELIX HERE
    5. Mutate Residues: In the vertical Menu -->MUTATE and AUTOFIT--> Click residue and Mutate

    OPTIONAL: Model Building Tutorial by Michael Sawaya (Powerpoint Presentation)