X-Ray Crystallography

  1. Analysis and Interpretation of Crystal Structures
    1. Describing the Atomic Model
      1. Atomic Coordinates and Connectivity
        1. Coordinate Files and Formats
          1. Bonding Networks
          2. Thermal Motion and Disorder
            1. Interpretation of B-factors
              1. Types of Disorder
              2. Conformational Analysis
                1. Alternate Conformations
                  1. Domain Movements
                2. Molecular Geometry and Interactions
                  1. Covalent Bonds
                    1. Bond Lengths and Angles
                      1. Planarity and Chirality
                      2. Non-covalent Interactions
                        1. Hydrogen Bonds
                          1. Donor and Acceptor Identification
                            1. Hydrogen Bond Networks
                            2. Van der Waals Forces
                              1. Contact Distances
                              2. Ionic Interactions
                                1. Salt Bridges
                                2. Hydrophobic Interactions
                                  1. Hydrophobic Core Analysis
                              3. Biological Macromolecule Analysis
                                1. Protein Folds and Domains
                                  1. Classification of Folds
                                    1. Domain Organization
                                    2. Enzyme Active Sites and Mechanisms
                                      1. Identification of Catalytic Residues
                                        1. Substrate Binding Modes
                                        2. Protein-Ligand Interactions
                                          1. Binding Site Identification
                                            1. Affinity and Specificity
                                            2. Protein-Nucleic Acid Complexes
                                              1. DNA Recognition
                                                1. RNA Recognition
                                                  1. Protein-DNA Interfaces
                                                    1. Protein-RNA Interfaces
                                                    2. Allosteric Regulation
                                                      1. Conformational Changes
                                                        1. Effector Binding Sites
                                                      2. Materials Science Analysis
                                                        1. Phase Identification and Quantification
                                                          1. Phase Diagrams
                                                            1. Quantitative Analysis Methods
                                                            2. Lattice Parameters and Strain
                                                              1. Unit Cell Refinement
                                                                1. Strain Analysis
                                                                2. Relationship between Crystal Structure and Material Properties
                                                                  1. Mechanical Properties
                                                                    1. Electronic Properties
                                                                      1. Optical Properties

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                                                                  5. Model Building, Refinement, and Validation

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                                                                  7. Advanced Topics and Related Techniques