International Tables for Crystallography Volume F: Crystallography of biological macromolecules

Description

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]. 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