X-Ray Crystallography

  1. Model Building, Refinement, and Validation
    1. Electron Density Maps
      1. Calculation of Initial Maps
        1. Fo Maps
          1. 2Fo-Fc Maps
            1. Fo-Fc Difference Maps
            2. Interpretation of Electron Density
              1. Identifying Atomic Positions
                1. Recognizing Map Artifacts
                2. Map Visualization and Contouring
                  1. Software Tools
                    1. Contour Level Selection
                  2. Atomic Model Building
                    1. Tracing the Main Chain
                      1. Backbone Tracing
                        1. Sequence Assignment
                        2. Fitting Side Chains or Molecular Fragments
                          1. Rotamer Libraries
                            1. Alternate Conformations
                            2. Placement of Solvent Molecules
                              1. Water Identification
                                1. Ions and Ligands
                              2. Structure Refinement
                                1. The Goal of Refinement
                                  1. Improving Model-Data Agreement
                                    1. Minimizing Model Bias
                                    2. Least-Squares Minimization
                                      1. Refinement Algorithms
                                        1. Weighting Schemes
                                        2. Refinement Parameters
                                          1. Atomic Coordinates
                                            1. Displacement Parameters
                                              1. Isotropic B-factors
                                                1. Anisotropic B-factors
                                                2. Occupancy
                                                  1. Partial Occupancy
                                                    1. Alternate Conformations
                                                  2. The R-factor and R-free
                                                    1. Definitions and Calculation
                                                      1. Interpretation and Target Values
                                                      2. Iterative Cycles of Refinement and Rebuilding
                                                        1. Map Inspection and Model Correction
                                                          1. Convergence Criteria
                                                        2. Structure Validation
                                                          1. Assessment of Geometric Quality
                                                            1. Bond Lengths and Angles
                                                              1. Torsion Angles
                                                                1. The Ramachandran Plot
                                                                  1. Allowed and Disallowed Regions
                                                                  2. Steric Clashes
                                                                    1. Clashscore
                                                                  3. Agreement with Experimental Data
                                                                    1. Real-space Correlation Coefficient
                                                                      1. Map-Model Fit
                                                                      2. Deposition in Public Databases
                                                                        1. Protein Data Bank
                                                                          1. Deposition Process
                                                                            1. Validation Reports
                                                                            2. Cambridge Structural Database
                                                                              1. Deposition Process
                                                                                1. Data Requirements

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                                                                          4. Data Processing and Structure Solution

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                                                                          6. Analysis and Interpretation of Crystal Structures