International Tables for Crystallography Volume F is an expert guide to macromolecular crystallography for the structural biologist. It was commissioned by the International Union of Crystallography in recognition of the extraordinary contributions that knowledge of macromolecular structure has made, and will make, to the analysis of biological systems, from enzyme catalysis to the workings of a whole cell. The volume covers all stages of a crystallographic analysis from the preparation of recombinant proteins, through crystallization, diffraction data collection, phase determination, structure validation and structure analysis.
Although the volume is written for experienced scientists, it is recognized that the reader is more likely to be a biologist interested in structure than a classical crystallographer interested in biology. Thus, there are chapters on the fundamentals, history and current perspectives of macromolecular crystallography, as well as on useful programs and databases such as the Protein Data Bank. Each chapter is written by one or more internationally recognized experts.
This second edition features 19 new articles and many articles from the first edition have been revised. The new articles cover topics such as standard definitions for quality indicators, expression of membrane proteins, protein engineering, high-throughput crystallography, imaging of whole cells, radiation damage, merohedral twinning, low-resolution ab initio phasing, robotic crystal loading and halogen interactions in biological crystal structures. There are also new articles on relevant software, including software for electron microscopy. These enhancements will ensure that Volume F continues to be a key reference for macromolecular crystallographers and structural biologists.
This edition of Volume F has been reviewed by J. S. Ferrara [ACA RefleXions, Winter 2012 issue, 24-25]. The first edition of Volume F was reviewed by C. W. Carter Jr [Structure (2002). 10, 289] and J. J. Müller [Z. Kristallogr. (2002). 217, 627-628].
Author(s): E. Arnold, D. M. Himmel, M. G. Rossmann (Eds.)
Series: IUCr Series. International Tables of Crystallography
Edition: 2
Publisher: John Wiley & Sons, Ltd
Year: 2011
Language: English
Pages: 886
Tags: crystallography
Contributing authors
Contents
Preface
Preface to the second edition
Chapter 1.1. Overview
Chapter 1.2. Historical background
Chapter 1.3. Macromolecular crystallography and medicine
Chapter 1.4. Perspectives for the future
Chapter 2.1. Introduction to basic crystallography
Chapter 2.2. Quality indicators in macromolecular crystallography: definitions and applications
Chapter 3.1. Preparing recombinant proteins for X-ray crystallography
Chapter 3.2. Expression and purification of membrane proteins for structural studies
Chapter 4.1. General methods
Chapter 4.2. Crystallization of membrane proteins
Chapter 4.3. Application of protein engineering to enhance crystallizability and improve crystal properties
Chapter 4.4. High-throughput X-ray crystallography
Chapter 5.1. Crystal morphology, optical properties of crystals and crystal mounting
Chapter 5.2. Crystal-density measurements
Chapter 6.1. X-ray sources
Chapter 6.2. Neutron sources
Chapter 7.1. Comparison of X-ray detectors
Chapter 7.2. CCD detectors
Chapter 8.1. Synchrotron-radiation instrumentation, methods and scientific utilization
Chapter 8.2. Laue crystallography: time-resolved studies
Chapter 9.1. Principles of monochromatic data collection
Chapter 9.2. Robotic crystal loading
Chapter 9.3. X-ray diffraction imaging of whole cells
Chapter 10.1. Introduction to cryocrystallography
Chapter 10.2. Cryocrystallography techniques and devices
Chapter 10.3. Radiation damage
Chapter 11.1. Automatic indexing of oscillation images
Chapter 11.2. Integration of macromolecular diffraction data
Chapter 11.3. Integration, scaling, space-group assignment and post refinement
Chapter 11.4. DENZO and SCALEPACK
Chapter 11.5. The use of partially recorded reflections for post refinement, scaling and averaging X-ray diffraction data
Chapter 11.6. XDS
Chapter 11.7. Detecting twinning by merohedry
Chapter 12.1. The preparation of heavy-atom derivatives of protein crystals for use in multiple isomorphous replacement and anomalous scattering
Chapter 12.2. Locating heavy-atom sites
Chapter 13.1. Noncrystallographic symmetry
Chapter 13.2. Rotation functions
Chapter 13.3. Translation functions
Chapter 13.4. Noncrystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension
Chapter 13.5. Molecular replacement with MOLREP
Chapter 14.1. Heavy-atom location and phase determination with single-wavelength diffraction data
Chapter 14.2. Multiwavelength anomalous diffraction
Chapter 14.3. Automated MAD and MIR structure solution
Chapter 15.1. Phase improvement by iterative density modification
Chapter 15.2. Model phases: probabilities, bias and maps
Chapter 15.3. DM/DMMULTI software for phase improvement by density modification
Chapter 16.1. Ab initio phasing
Chapter 16.2. The maximum-entropy method
Chapter 16.3. Ab initio phasing of low-resolution Fourier syntheses
Chapter 17.1. Macromolecular model building and validation using Coot
Chapter 17.2. Molecular graphics and animation
Chapter 18.1. Introduction to refinement
Chapter 18.2. Enhanced macromolecular refinement by simulated annealing
Chapter 18.3. Structure quality and target parameters
Chapter 18.4. Refinement at atomic resolution
Chapter 18.5. Coordinate uncertainty
Chapter 18.6. CNS, a program system for structure-determination and refinement
Chapter 18.7. The TNT refinement package
Chapter 18.8. ARP/wARP – automated model building and refinement
Chapter 18.9. Macromolecular applications of SHELX
Chapter 18.10. PrimeX and the Schro¨ dinger computational chemistry suite of programs
Chapter 18.11. PHENIX: a comprehensive Python-based system for macromolecular structure solution
Chapter 18.12. Structure determination in the presence of twinning by merohedry
Chapter 19.1. Neutron crystallography: methods and information content
Chapter 19.2. Electron diffraction of protein crystals
Chapter 19.3. Small-angle X-ray scattering
Chapter 19.4. Small-angle neutron scattering
Chapter 19.5. Fibre diffraction
Chapter 19.6. Electron cryomicroscopy of biological macromolecules
Chapter 19.7. Nuclear magnetic resonance (NMR) spectroscopy
Chapter 19.8. Use of SPIDER and SPIRE in image reconstruction
Chapter 19.9. Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D
Chapter 19.10. Single-particle reconstruction with EMAN
Chapter 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin
Chapter 20.2. Molecular-dynamics simulations of biological macromolecules
Chapter 21.1. Validation of protein crystal structures
Chapter 21.2. Assessing the quality of macromolecular structures
Chapter 21.3. Detection of errors in protein models
Chapter 21.4. PROCHECK: validation of protein-structure coordinates
Chapter 21.5. KiNG and kinemages
Chapter 21.6. MolProbity: all-atom structure validation for macromolecular crystallography
Chapter 22.1. Protein geometry: volumes, areas and distances
Chapter 22.2. Molecular surfaces: calculations, uses and representations
Chapter 22.3. Hydrogen bonding in biological macromolecules
Chapter 22.4. Electrostatic interactions in proteins
Chapter 22.5. The relevance of the Cambridge Structural Database in protein crystallography
Chapter 23.1. Protein-fold classification
Chapter 23.2. Locating domains in three-dimensional structures
Chapter 23.3. Protein–ligand interactions
Chapter 23.4. Nucleic acids
Chapter 23.5. Solvent structure
Chapter 23.6. Halogen interactions in biomolecular crystal structures
Chapter 24.1. The Worldwide Protein Data Bank
Chapter 24.2. The Nucleic Acid Database
Chapter 24.3. The Biological Macromolecule Crystallization Database
Chapter 25.1. How the structure of lysozyme was actually determined
Subject index
