Preface to the Second Edition |
Preface to the First Edition |
Model and Molecule / 1.: |
An Overview of Protein Crystallography / 2.: |
Introduction / I.: |
Obtaining an image of a microscopic object / A.: |
Obtaining images of molecules / B.: |
A thumbnail sketch of protein crystallography / C.: |
Crystals / II.: |
The nature of crystals |
Growing crystals |
Collecting X-ray data / III.: |
Diffraction / IV.: |
Simple objects |
Arrays of simple objects: Real and reciprocal lattices |
Intensities of reflections |
Arrays of complex objects / D.: |
Three-dimensional arrays / E.: |
Coordinate systems in crystallography / V.: |
The mathematics of crystallography: A brief description / VI.: |
Wave equations: Periodic functions |
Complicated periodic functions: Fourier series |
Structure factors: Wave descriptions of X-ray reflections |
Electron-density maps |
Electron density from structure factors |
Electron density from measured reflections / F.: |
Obtaining a model / G.: |
Protein Crystals / 3.: |
Properties of protein crystals |
Size, structural integrity, and mosaicity |
Multiple crystalline forms |
Water content |
Evidence that solution and crystal structures are similar |
Proteins retain their function in the crystal |
X-ray structures are compatible with other structural evidence |
Other evidence |
Growing protein crystals |
Growing crystals: Basic procedure |
Growing derivative crystals |
Finding optimal conditions for crystal growth |
Judging crystal quality |
Mounting crystals for data collection |
Collecting Diffraction Data / 4.: |
Geometric principles of diffraction |
The generalized unit cell |
Indices of the atomic planes in a crystal |
Conditions that produce diffraction: Bragg's law |
The reciprocal lattice |
Bragg's law in reciprocal space |
The number of measurable reflections |
Unit-cell dimensions |
Unit-cell symmetry / H.: |
Collecting X-ray diffraction data |
X-ray sources |
Detectors |
Diffractometers and cameras |
Scaling and postrefinement of intensity data |
Determining unit-cell dimensions |
Symmetry and the strategy of collecting data |
Summary |
From Diffraction Data to Electron Density / 5.: |
Fourier series and the Fourier transform |
One-dimensional waves |
Three-dimensional waves |
The Fourier transform: General features |
Fourier this and Fourier that: Review |
Fourier mathematics and diffraction |
Stucture factor as a Fourier series |
Electron density as a Fourier series |
Computing electron density from data |
The phase problem |
The meaning of the Fourier equations |
Reflections as Fourier terms: Equation (5.18) |
Computing structure factors from a model: Equations (5.15) and (5.16) |
Systematic absences in the diffraction pattern: Equation (5.15) |
Summary: From data to density |
Obtaining Phases / 6.: |
Two-dimensional representation of structure factors |
Complex numbers in two dimensions |
Structure factors as complex vectors |
Electron density as a function of intensities and phases |
The heavy-atom method (isomorphous replacement) |
Preparing heavy-atom derivatives |
Obtaining phases from heavy-atom data |
Locating heavy atoms in the unit cell |
Anomalous scattering |
The measurable effects of anomalous scattering |
Extracting phases from anomalous scattering data |
Multiwavelength anomalous diffraction phasing |
Anomalous scattering and the hand problem |
Direct phasing: Application of methods from small-molecule crystallography |
Molecular replacement: Related proteins as phasing models |
Isomorphous phasing models |
Nonisomorphous phasing models |
Separate searches for orientation and location |
Monitoring the search |
Iterative improvement of phases (preview of Chapter 7) |
Obtaining and Judging the Molecular Model / 7.: |
Iterative improvement of maps and models: Overview |
First maps |
Resources for the first map |
Displaying and examining the map |
Improving the map |
The model becomes molecular |
New phases from the molecular model |
Minimizing bias from the model |
Map fitting |
Structure refinement |
Least-squares methods |
Crystallographic refinement |
Additional refinement parameters |
Local minima and radius of convergence |
Molecular energy and motion in refinement |
Convergence to a final structure |
Producing the final map and model |
Guides to convergence |
Sharing the model / VII.: |
A User's Guide to Crystallographic Models / 8.: |
Judging the quality and usefulness of the refined model |
Structural parameters |
Resolution and precision of atomic positions |
Vibration and disorder |
Other limitations of crystallographic models |
Reading a crystallography paper |
Annotated excerpts of the preliminary (8/91) paper |
Annotated excerpts from the full structure determination (4/92) paper |
Other Diffraction Methods / 9.: |
Fiber diffraction |
Diffraction by amorphous materials (scattering) |
Neutron diffraction |
Electron diffraction |
Lane diffraction and time-resolved crystallography |
Conclusion |
Other Kinds of Macromolecular Models / 10.: |
NMR models |
Principles |
Assigning resonances |
Determining conformation |
PDB files for NMR models |
Judging model quality |
Homology models |
Databases of homology models |
Other theoretical models |
Tools for Studying Macromolecules / 11.: |
Computer models of molecules |
Two-dimensional images from coordinates |
Into three dimensions: Basic modeling operations |
Three-dimensional display and perception |
Types of graphical models |
Touring a typical molecular modeling program |
Importing and exporting coordinates files |
Loading and saving models |
Viewing models |
Editing and labeling the display |
Coloring |
Measuring |
Exploring structural change |
Exploring the molecular surface |
Exploring intermolecular interactions: Multiple models |
Displaying crystal packing / J.: |
Building models from scratch / K.: |
Other tools for studying structure |
Tools for structure analysis |
Tools for modeling protein action |
A final note |
Index |
Preface to the Second Edition |
Preface to the First Edition |
Model and Molecule / 1.: |