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Preface to the Third Edition | |
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Preface to the Second Edition | |
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Preface to the First Edition | |
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Model and Molecule | |
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An Overview of Protein Crystallography | |
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Introduction | |
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Obtaining an image of a microscopic object | |
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Obtaining images of molecules | |
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A thumbnail sketch of protein crystallography | |
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Crystals | |
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The nature of crystals | |
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Growing crystals | |
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Collecting X-ray data | |
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Diffraction | |
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Simple objects | |
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Arrays of simple objects: Real and reciprocal lattices | |
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Intensities of reflections | |
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Arrays of complex objects | |
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Three-dimensional arrays | |
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Coordinate systems in crystallography | |
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The mathematics of crystallography: A brief description | |
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Wave equations: Periodic functions | |
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Complicated periodic functions: Fourier series and sums | |
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Structure factors: Wave descriptions of X-ray reflections | |
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Electron-density maps | |
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Electron density from structure factors | |
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Electron density from measured reflections | |
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Obtaining a model | |
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Protein Crystals | |
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Properties of protein crystals | |
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Introduction | |
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Size, structural integrity, and mosaicity | |
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Multiple crystalline forms | |
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Water content | |
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Evidence that solution and crystal structures are similar | |
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Proteins retain their function in the crystal | |
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X-ray structures are compatible with other structural evidence | |
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Other evidence | |
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Growing protein crystals | |
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Introduction | |
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Growing crystals: Basic procedure | |
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Growing derivative crystals | |
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Finding optimal conditions for crystal growth | |
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Judging crystal quality | |
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Mounting crystals for data collection | |
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Collecting Diffraction Data | |
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Introduction | |
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Geometric principles of diffraction | |
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The generalized unit cell | |
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Indices of the atomic planes in a crystal | |
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Conditions that produce diffraction: Bragg's law | |
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The reciprocal lattice | |
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Bragg's law in reciprocal space | |
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Number of measurable reflections | |
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Unit-cell dimensions | |
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Unit-cell symmetry | |
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Collecting X-ray diffraction data | |
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Introduction | |
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X-ray sources | |
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Detectors | |
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Cameras | |
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Scaling and postrefinement of intensity data | |
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Determining unit-cell dimensions | |
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Symmetry and the strategy of collecting data | |
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Summary | |
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From Diffraction Data to Electron Density | |
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Introduction | |
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Fourier sums and the Fourier transform | |
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One-dimensional waves | |
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Three-dimensional waves | |
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The Fourier transform: General features | |
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Fourier this and Fourier that: Review | |
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Fourier mathematics and diffraction | |
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Structure factor as a Fourier sum | |
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Electron density as a Fourier sum | |
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Computing electron density from data | |
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The phase problem | |
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Meaning of the Fourier equations | |
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Reflections as terms in a Fourier sum: Eq. (5.18) | |
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Computing structure factors from a model: Eq. (5.15) and Eq. (5.16) | |
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Systematic absences in the diffraction pattern: Eq. (5.15) | |
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Summary: From data to density | |
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Obtaining Phases | |
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Introduction | |
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Two-dimensional representation of structure factors | |
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Complex numbers in two dimensions | |
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Structure factors as complex vectors | |
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Electron density as a function of intensities and phases | |
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Isomorphous replacement | |
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Preparing heavy-atom derivatives | |
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Obtaining phases from heavy-atom data | |
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Locating heavy atoms in the unit cell | |
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Anomalous scattering | |
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Introduction | |
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Measurable effects of anomalous scattering | |
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Extracting phases from anomalous scattering data | |
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Summary | |
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Multiwavelength anomalous diffraction phasing | |
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Anomalous scattering and the hand problem | |
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Direct phasing: Application of methods from small-molecule crystallography | |
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Molecular replacement: Related proteins as phasing models | |
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Introduction | |
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Isomorphous phasing models | |
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Nonisomorphous phasing models | |
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Separate searches for orientation and location | |
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Monitoring the search | |
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Summary of molecular replacement | |
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Iterative improvement of phases (preview of Chapter 7) | |
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Obtaining and Judging the Molecular Model | |
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Introduction | |
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Iterative improvement of maps and models-overview | |
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First maps | |
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Resources for the first map | |
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Displaying and examining the map | |
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Improving the map | |
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The Model becomes molecular | |
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New phases from the molecular model | |
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Minimizing bias from the model | |
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Map fitting | |
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Structure refinement | |
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Least-squares methods | |
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Crystallographic refinement by least squares | |
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Additional refinement parameters | |
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Local minima and radius of convergence | |
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Molecular energy and motion in refinement | |
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Bayesian methods: Ensembles of models | |
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Convergence to a final model | |
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Producing the final map and model | |
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Guides to convergence | |
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Sharing the model | |
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A User's Guide to Crystallographic Models | |
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Introduction | |
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Judging the quality and usefulness of the refined model | |
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Structural parameters | |
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Resolution and precision of atomic positions | |
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Vibration and disorder | |
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Other limitations of crystallographic models | |
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Online validation tools: Do it yourself! | |
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Summary | |
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Reading a crystallography paper | |
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Introduction | |
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Annotated excerpts of the preliminary (8/91) paper | |
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Annotated excerpts from the full structure-determination (4/92) paper | |
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Summary | |
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Other Diffraction Methods | |
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Introduction | |
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Fiber diffraction | |
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Diffraction by amorphous materials (scattering) | |
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Neutron diffraction | |
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Electron diffraction and cryo-electron microscopy | |
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Laue diffraction and time-resolved crystallography | |
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Summary | |
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Other Kinds of Macromolecular Models | |
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Introduction | |
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NMR models | |
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Introduction | |
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Principles | |
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Assigning resonances | |
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Determining conformation | |
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PDB files for NMR models | |
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Judging model quality | |
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Homology models | |
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Introduction | |
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Principles | |
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Databases of homology models | |
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Judging model quality | |
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Other theoretical models | |
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Tools for Studying Macromolecules | |
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Introduction | |
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Computer models of molecules | |
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Two-dimensional images from coordinates | |
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Into three dimensions: Basic modeling operations | |
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Three-dimensional display and perception | |
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Types of graphical models | |
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Touring a molecular modeling program | |
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Importing and exporting coordinate files | |
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Loading and saving models | |
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Viewing models | |
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Editing and labeling the display | |
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Coloring | |
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Measuring | |
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Exploring structural change | |
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Exploring the molecular surface | |
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Exploring intermolecular interactions: Multiple models | |
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Displaying crystal packing | |
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Building models from scratch | |
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Scripts and macros: Automating routine structure analysis | |
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Other tools for studying structure | |
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Tools for structure analysis and validation | |
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Tools for modeling protein action | |
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Final note | |
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Viewing Stereo Images | |
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Index | |