Crystallography Made Crystal Clear A Guide for Users of Macromolecular Models

ISBN-10: 0125870736

ISBN-13: 9780125870733

Edition: 3rd 2006 (Revised)

Authors: Gale Rhodes

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This new edition explains to graduate students and researchers the basics of chrystallography for all macromolecules. It contains new material, concentrating on the advances in the desktops programs used for modelling.
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Book details

List price: $63.95
Edition: 3rd
Copyright year: 2006
Publisher: Elsevier Science & Technology Books
Publication date: 2/16/2006
Binding: Paperback
Pages: 352
Size: 6.00" wide x 8.75" long x 0.50" tall
Weight: 1.430
Language: English

Gale Rhodes earned a B.S. in applied mathematics at North Carolina State University, and then a Ph.D. in Chemistry at the University of North Carolina. He is currently a professor of chemistry at the University of Southern Maine, Portland. His main duty, and first love, is teaching undergraduate biochemistry. He has received awards for outstanding teaching at three different colleges. His best known publication is the first edition of Crystallography Made Crystal Clear, which received very complimentary reviews in several journals. He has also published three book chapters, three book reviews, and about 30 articles on diverse subjects, including research articles in biochemistry, and articles on chemistry, science, and interdisciplinary education.

Preface to the Third Edition
Preface to the Second Edition
Preface to the First Edition
Model and Molecule
An Overview of Protein Crystallography
Obtaining an image of a microscopic object
Obtaining images of molecules
A thumbnail sketch of protein crystallography
The nature of crystals
Growing crystals
Collecting X-ray data
Simple objects
Arrays of simple objects: Real and reciprocal lattices
Intensities of reflections
Arrays of complex objects
Three-dimensional arrays
Coordinate systems in crystallography
The mathematics of crystallography: A brief description
Wave equations: Periodic functions
Complicated periodic functions: Fourier series and sums
Structure factors: Wave descriptions of X-ray reflections
Electron-density maps
Electron density from structure factors
Electron density from measured reflections
Obtaining a model
Protein Crystals
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
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
Number of measurable reflections
Unit-cell dimensions
Unit-cell symmetry
Collecting X-ray diffraction data
X-ray sources
Scaling and postrefinement of intensity data
Determining unit-cell dimensions
Symmetry and the strategy of collecting data
From Diffraction Data to Electron Density
Fourier sums 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
Structure factor as a Fourier sum
Electron density as a Fourier sum
Computing electron density from data
The phase problem
Meaning of the Fourier equations
Reflections as terms in a Fourier sum: Eq. (5.18)
Computing structure factors from a model: Eq. (5.15) and Eq. (5.16)
Systematic absences in the diffraction pattern: Eq. (5.15)
Summary: From data to density
Obtaining Phases
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
Isomorphous replacement
Preparing heavy-atom derivatives
Obtaining phases from heavy-atom data
Locating heavy atoms in the unit cell
Anomalous scattering
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
Summary of molecular replacement
Iterative improvement of phases (preview of Chapter 7)
Obtaining and Judging the Molecular Model
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 by least squares
Additional refinement parameters
Local minima and radius of convergence
Molecular energy and motion in refinement
Bayesian methods: Ensembles of models
Convergence to a final model
Producing the final map and model
Guides to convergence
Sharing the model
A User's Guide to Crystallographic Models
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
Online validation tools: Do it yourself!
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
Fiber diffraction
Diffraction by amorphous materials (scattering)
Neutron diffraction
Electron diffraction and cryo-electron microscopy
Laue diffraction and time-resolved crystallography
Other Kinds of Macromolecular Models
NMR models
Assigning resonances
Determining conformation
PDB files for NMR models
Judging model quality
Homology models
Databases of homology models
Judging model quality
Other theoretical models
Tools for Studying Macromolecules
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 molecular modeling program
Importing and exporting coordinate files
Loading and saving models
Viewing models
Editing and labeling the display
Exploring structural change
Exploring the molecular surface
Exploring intermolecular interactions: Multiple models
Displaying crystal packing
Building models from scratch
Scripts and macros: Automating routine structure analysis
Other tools for studying structure
Tools for structure analysis and validation
Tools for modeling protein action
Final note
Viewing Stereo Images
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