International Tables for Crystallography Volume F: Crystallography of biological macromolecules F

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 3 Contents 7 Preface 24 Preface to the second edition 25 Chapter 1.1. Overview 26 Chapter 1.2. Historical background 30 Chapter 1.3. Macromolecular crystallography and medicine 38 Chapter 1.4. Perspectives for the future 64 Chapter 2.1. Introduction to basic crystallography 70 Chapter 2.2. Quality indicators in macromolecular crystallography: definitions and applications 89 Chapter 3.1. Preparing recombinant proteins for X-ray crystallography 100 Chapter 3.2. Expression and purification of membrane proteins for structural studies 117 Chapter 4.1. General methods 124 Chapter 4.2. Crystallization of membrane proteins 147 Chapter 4.3. Application of protein engineering to enhance crystallizability and improve crystal properties 154 Chapter 4.4. High-throughput X-ray crystallography 165 Chapter 5.1. Crystal morphology, optical properties of crystals and crystal mounting 170 Chapter 5.2. Crystal-density measurements 177 Chapter 6.1. X-ray sources 184 Chapter 6.2. Neutron sources 193 Chapter 7.1. Comparison of X-ray detectors 202 Chapter 7.2. CCD detectors 208 Chapter 8.1. Synchrotron-radiation instrumentation, methods and scientific utilization 214 Chapter 8.2. Laue crystallography: time-resolved studies 230 Chapter 9.1. Principles of monochromatic data collection 236 Chapter 9.2. Robotic crystal loading 256 Chapter 9.3. X-ray diffraction imaging of whole cells 259 Chapter 10.1. Introduction to cryocrystallography 266 Chapter 10.2. Cryocrystallography techniques and devices 274 Chapter 10.3. Radiation damage 281 Chapter 11.1. Automatic indexing of oscillation images 288 Chapter 11.2. Integration of macromolecular diffraction data 291 Chapter 11.3. Integration, scaling, space-group assignment and post refinement 297 Chapter 11.4. DENZO and SCALEPACK 307 Chapter 11.5. The use of partially recorded reflections for post refinement, scaling and averaging X-ray diffraction data 321 Chapter 11.6. XDS 329 Chapter 11.7. Detecting twinning by merohedry 336 Chapter 12.1. The preparation of heavy-atom derivatives of protein crystals for use in multiplei somorphous replacement and anomalous scattering 342 Chapter 12.2. Locating heavy-atom sites 352 Chapter 13.1. Noncrystallographic symmetry 358 Chapter 13.2. Rotation functions 365 Chapter 13.3. Translation functions 372 Chapter 13.4. Noncrystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension 377 Chapter 13.5. Molecular replacement with MOLREP 389 Chapter 14.1. Heavy-atom location and phase determination with single-wavelength diffraction data 392 Chapter 14.2. Multiwavelength anomalous diffraction 398 Chapter 14.3. Automated MAD and MIR structure solution 404 Chapter 15.1. Phase improvement by iterative density modification 410 Chapter 15.2. Model phases: probabilities, bias and maps 426 Chapter 15.3. DM/DMMULTI software for phase improvement by density modification 432 Chapter 16.1. Ab initio phasing 438 Chapter 16.2. The maximum-entropy method 458 Chapter 16.3. Ab initio phasing of low-resolution Fourier syntheses 462 Chapter 17.1. Macromolecular model building and validation using Coot 468 Chapter 17.2. Molecular graphics and animation 473 Chapter 18.1. Introduction to refinement 484 Chapter 18.2. Enhanced macromolecular refinement by simulated annealing 491 Chapter 18.3. Structure quality and target parameters 499 Chapter 18.4. Refinement at atomic resolution 510 Chapter 18.5. Coordinate uncertainty 524 Chapter 18.6. CNS, a program system for structure-determination and refinement 537 Chapter 18.7. The TNT refinement package 545 Chapter 18.8. ARP/wARP – automated model building and refinement 550 Chapter 18.9. Macromolecular applications of SHELX 554 Chapter 18.10. PrimeX and the Schro ̈ dinger computational chemistry suite of programs 559 Chapter 18.11. PHENIX: a comprehensive Python-based system for macromolecular structure solution 564 Chapter 18.12. Structure determination in the presence of twinning by merohedry 573 Chapter 19.1. Neutron crystallography: methods and information content 578 Chapter 19.2. Electron diffraction of protein crystals 582 Chapter 19.3. Small-angle X-ray scattering 588 Chapter 19.4. Small-angle neutron scattering 600 Chapter 19.5. Fibre diffraction 608 Chapter 19.6. Electron cryomicroscopy of biological macromolecules 618 Chapter 19.7. Nuclear magnetic resonance (NMR) spectroscopy 640 Chapter 19.8. Use of SPIDER and SPIRE in image reconstruction 645 Chapter 19.9. Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D 649 Chapter 19.10. Single-particle reconstruction with EMAN 654 Chapter 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin 658 Chapter 20.2. Molecular-dynamics simulations of biological macromolecules 667 Chapter 21.1. Validation of protein crystal structures 674 Chapter 21.2. Assessing the quality of macromolecular structures 687 Chapter 21.3. Detection of errors in protein models 702 Chapter 21.4. PROCHECK: validation of protein-structure coordinates 709 Chapter 21.5. KiNG and kinemages 713 Chapter 21.6. MolProbity: all-atom structure validation for macromolecular crystallography 719 Chapter 22.1. Protein geometry: volumes, areas and distances 728 Chapter 22.2. Molecular surfaces: calculations, uses and representations 738 Chapter 22.3. Hydrogen bonding in biological macromolecules 746 Chapter 22.4. Electrostatic interactions in proteins 755 Chapter 22.5. The relevance of the Cambridge Structural Database in protein crystallography 761 Chapter 23.1. Protein-fold classification 774 Chapter 23.2. Locating domains in three-dimensional structures 777 Chapter 23.3. Protein–ligand interactions 780 Chapter 23.4. Nucleic acids 791 Chapter 23.5. Solvent structure 825 Chapter 23.6. Halogen interactions in biomolecular crystal structures 846 Chapter 24.1. The Worldwide Protein Data Bank 852 Chapter 24.2. The Nucleic Acid Database 858 Chapter 24.3. The Biological Macromolecule Crystallization Database 863 Chapter 25.1. How the structure of lysozyme was actually determined 870 Subject index 899 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 This volume was commissioned by the International Union of Crystallography (IUCr) 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, and to the growing field of structural genomics.