(International Tables) Crystallography of biological macromolecules

International Tables for Crystallography
Volume F: Crystallography of biological macromolecules

First online edition (2006) ISBN: 978-0-7923-6857-1 eISBN: 978-1-4020-5416-7 doi: 10.1107/97809553602060000106

Edited by M. G. Rossmann and E. Arnold

Preface (p. xxiii) | html | pdf |
E. Arnold and M. G. Rossmann

Part 1. Introduction
- 1.1. Overview (pp. 1-3) | html | pdf | chapter contents |
  E. Arnold and M. G. Rossmann
- 1.2. Historical background (pp. 4-9) | html | pdf | chapter contents |
  M. G. Rossmann
  - 1.2.1. Introduction (p. 4) | html | pdf |
  - 1.2.2. 1912 to the 1950s (pp. 4-5) | html | pdf |
  - 1.2.3. The first investigations of biological macromolecules (p. 5) | html | pdf |
  - 1.2.4. Globular proteins in the 1950s (pp. 5-7) | html | pdf |
  - 1.2.5. The first protein structures (1957 to the 1970s) (pp. 7-8) | html | pdf |
  - 1.2.6. Technological developments (1958 to the 1980s) (pp. 8-9) | html | pdf |
  - 1.2.7. Meetings (p. 9) | html | pdf |
  - References | html | pdf |
- 1.3. Macromolecular crystallography and medicine (pp. 10-25) | html | pdf | chapter contents |
  W. G. J. Hol and C. L. M. J. Verlinde
  - 1.3.1. Introduction (p. 10) | html | pdf |
  - 1.3.2. Crystallography and medicine (pp. 10-11) | html | pdf |
  - 1.3.3. Crystallography and genetic diseases (pp. 11-12) | html | pdf |
  - 1.3.4. Crystallography and development of novel pharmaceuticals (pp. 12-24) | html | pdf |
  - 1.3.5. Vaccines, immunology and crystallography (pp. 24-25) | html | pdf |
  - 1.3.6. Outlook and dreams (p. 25) | html | pdf |
  - References | html | pdf |
- 1.4. Perspectives for the future (pp. 26-43) | html | pdf | chapter contents |
  E. Arnold and M. G. Rossmann
  - 1.4.1. Gazing into the crystal ball (pp. 26-27) | html | pdf |
    E. Arnold
  - 1.4.2. Brief comments on Gazing into the crystal ball (p. 27) | html | pdf |
    M. G. Rossmann

Part 2. Basic crystallography
- 2.1. Introduction to basic crystallography (pp. 45-63) | html | pdf | chapter contents |
  J. Drenth
  - 2.1.1. Crystals (pp. 45-46) | html | pdf |
  - 2.1.2. Symmetry (pp. 46-47) | html | pdf |
  - 2.1.3. Point groups and crystal systems (pp. 47-52) | html | pdf |
  - 2.1.4. Basic diffraction physics (pp. 52-57) | html | pdf |
  - 2.1.5. Reciprocal space and the Ewald sphere (pp. 57-58) | html | pdf |
  - 2.1.6. Mosaicity and integrated reflection intensity (pp. 58-59) | html | pdf |
  - 2.1.7. Calculation of electron density (pp. 59-60) | html | pdf |
  - 2.1.8. Symmetry in the diffraction pattern (pp. 60-61) | html | pdf |
  - 2.1.9. The Patterson function (pp. 61-62) | html | pdf |
  - References | html | pdf |

Part 3. Techniques of molecular biology
- 3.1. Preparing recombinant proteins for X-ray crystallography (pp. 65-80) | html | pdf | chapter contents |
  S. H. Hughes and A. M. Stock
  - 3.1.1. Introduction (p. 65) | html | pdf |
  - 3.1.2. Overview (p. 65) | html | pdf |
  - 3.1.3. Engineering an expression construct (pp. 66-67) | html | pdf |
  - 3.1.4. Expression systems (pp. 67-74) | html | pdf |
  - 3.1.5. Protein purification (pp. 75-77) | html | pdf |
  - 3.1.6. Characterization of the purified product (pp. 77-78) | html | pdf |
  - 3.1.7. Reprise (pp. 78-79) | html | pdf |
  - References | html | pdf |

Part 4. Crystallization
- 4.1. General methods (pp. 81-93) | html | pdf | chapter contents |
  R. Giegé and A. McPherson
  - 4.1.1. Introduction (p. 81) | html | pdf |
  - 4.1.2. Crystallization arrangements and methodologies (pp. 81-86) | html | pdf |
  - 4.1.3. Parameters that affect crystallization of macromolecules (pp. 86-88) | html | pdf |
  - 4.1.4. How to crystallize a new macromolecule (pp. 88-89) | html | pdf |
  - 4.1.5. Techniques for physical characterization of crystallization (pp. 89-91) | html | pdf |
  - 4.1.6. Use of microgravity (pp. 91-93) | html | pdf |
  - References | html | pdf |
- 4.2. Crystallization of membrane proteins (pp. 94-99) | html | pdf | chapter contents |
  H. Michel
  - 4.2.1. Introduction (p. 94) | html | pdf |
  - 4.2.2. Principles of membrane-protein crystallization (p. 94) | html | pdf |
  - 4.2.3. General properties of detergents relevant to membrane-protein crystallization (pp. 94-98) | html | pdf |
  - 4.2.4. The `small amphiphile concept' (p. 98) | html | pdf |
  - 4.2.5. Membrane-protein crystallization with the help of antibody Fv fragments (pp. 98-99) | html | pdf |
  - 4.2.6. Membrane-protein crystallization using cubic bicontinuous lipidic phases (p. 99) | html | pdf |
  - 4.2.7. General recommendations (p. 99) | html | pdf |
  - References | html | pdf |
- 4.3. Application of protein engineering to improve crystal properties (pp. 100-110) | html | pdf | chapter contents |
  D. R. Davies and A. Burgess Hickman
  - 4.3.1. Introduction (p. 100) | html | pdf |
  - 4.3.2. Improving solubility (pp. 100-101) | html | pdf |
  - 4.3.3. Use of fusion proteins (p. 101) | html | pdf |
  - 4.3.4. Mutations to accelerate crystallization (p. 101) | html | pdf |
  - 4.3.5. Mutations to improve diffraction quality (pp. 101-102) | html | pdf |
  - 4.3.6. Avoiding protein heterogeneity (p. 102) | html | pdf |
  - 4.3.7. Engineering crystal contacts to enhance crystallization in a particular crystal form (pp. 102-103) | html | pdf |
  - 4.3.8. Engineering heavy-atom sites (p. 103) | html | pdf |
  - References | html | pdf |

Part 5. Crystal properties and handling
- 5.1. Crystal morphology, optical properties of crystals and crystal mounting (pp. 111-116) | html | pdf | chapter contents |
  H. L. Carrell and J. P. Glusker
  - 5.1.1. Crystal morphology and optical properties (pp. 111-114) | html | pdf |
  - 5.1.2. Crystal mounting (pp. 114-116) | html | pdf |
  - References | html | pdf |
- 5.2. Crystal-density measurements (pp. 117-123) | html | pdf | chapter contents |
  E. M. Westbrook
  - 5.2.1. Introduction (p. 117) | html | pdf |
  - 5.2.2. Solvent in macromolecular crystals (p. 117) | html | pdf |
  - 5.2.3. Matthews number (p. 117) | html | pdf |
  - 5.2.4. Algebraic concepts (pp. 117-118) | html | pdf |
  - 5.2.5. Experimental estimation of hydration (p. 118) | html | pdf |
  - 5.2.6. Methods for measuring crystal density (pp. 118-121) | html | pdf |
  - 5.2.7. How to handle the solvent density (p. 121) | html | pdf |
  - References | html | pdf |

Part 6. Radiation sources and optics
- 6.1. X-ray sources (pp. 125-132) | html | pdf | chapter contents |
  U. W. Arndt
  - 6.1.1. Overview (p. 125) | html | pdf |
  - 6.1.2. Generation of X-rays (pp. 125-127) | html | pdf |
  - 6.1.3. Properties of the X-ray beam (pp. 127-129) | html | pdf |
  - 6.1.4. Beam conditioning (pp. 129-132) | html | pdf |
  - References | html | pdf |
- 6.2. Neutron sources (pp. 133-142) | html | pdf | chapter contents |
  B. P. Schoenborn and R. Knott
  - 6.2.1. Reactors (pp. 133-137) | html | pdf |
  - 6.2.2. Spallation neutron sources (pp. 137-139) | html | pdf |
  - 6.2.3. Summary (p. 139) | html | pdf |
  - References | html | pdf |

Part 7. X-ray detectors
- 7.1. Comparison of X-ray detectors (pp. 143-147) | html | pdf | chapter contents |
  S. M. Gruner, E. F. Eikenberry and M. W. Tate
  - 7.1.1. Commonly used detectors: general considerations (pp. 143-144) | html | pdf |
  - 7.1.2. Evaluating and comparing detectors (pp. 144-145) | html | pdf |
  - 7.1.3. Characteristics of different detector approaches (pp. 145-147) | html | pdf |
  - 7.1.4. Future detectors (p. 147) | html | pdf |
  - References | html | pdf |
- 7.2. CCD detectors (pp. 148-153) | html | pdf | chapter contents |
  M. W. Tate, E. F. Eikenberry and S. M. Gruner
  - 7.2.1. Overview (p. 148) | html | pdf |
  - 7.2.2. CCD detector assembly (pp. 148-149) | html | pdf |
  - 7.2.3. Calibration and correction (pp. 149-151) | html | pdf |
  - 7.2.4. Detector system integration (pp. 151-152) | html | pdf |
  - 7.2.5. Applications to macromolecular crystallography (p. 152) | html | pdf |
  - 7.2.6. Future of CCD detectors (p. 152) | html | pdf |
  - References | html | pdf |

Part 8. Synchrotron crystallography
- 8.1. Synchrotron-radiation instrumentation, methods and scientific utilization (pp. 155-166) | html | pdf | chapter contents |
  J. R. Helliwell
  - 8.1.1. Introduction (p. 155) | html | pdf |
  - 8.1.2. The physics of SR (p. 155) | html | pdf |
  - 8.1.3. Insertion devices (IDs) (pp. 155-156) | html | pdf |
  - 8.1.4. Beam characteristics delivered at the crystal sample (pp. 156-158) | html | pdf |
  - 8.1.5. Evolution of SR machines and experiments (pp. 158-161) | html | pdf |
  - 8.1.6. SR instrumentation (pp. 161-162) | html | pdf |
  - 8.1.7. SR monochromatic and Laue diffraction geometry (pp. 162-164) | html | pdf |
  - 8.1.8. Scientific utilization of SR in protein crystallography (pp. 164-166) | html | pdf |
  - References | html | pdf |
- 8.2. Laue crystallography: time-resolved studies (pp. 167-176) | html | pdf | chapter contents |
  K. Moffat
  - 8.2.1. Introduction (p. 167) | html | pdf |
  - 8.2.2. Principles of Laue diffraction (pp. 167-168) | html | pdf |
  - 8.2.3. Practical considerations in the Laue technique (pp. 168-170) | html | pdf |
  - 8.2.4. The time-resolved experiment (pp. 170-171) | html | pdf |
  - 8.2.5. Conclusions (p. 171) | html | pdf |
  - References | html | pdf |

Part 9. Monochromatic data collection
- 9.1. Principles of monochromatic data collection (pp. 177-195) | html | pdf | chapter contents |
  Z. Dauter and K. S. Wilson
  - 9.1.1. Introduction (p. 177) | html | pdf |
  - 9.1.2. The components of a monochromatic X-ray experiment (p. 177) | html | pdf |
  - 9.1.3. Data completeness (p. 177) | html | pdf |
  - 9.1.4. X-ray sources (pp. 177-178) | html | pdf |
  - 9.1.5. Goniostat geometry (pp. 178-179) | html | pdf |
  - 9.1.6. Basis of the rotation method (pp. 179-183) | html | pdf |
  - 9.1.7. Rotation method: geometrical completeness (pp. 183-188) | html | pdf |
  - 9.1.8. Crystal-to-detector distance (p. 188) | html | pdf |
  - 9.1.9. Wavelength (pp. 188-189) | html | pdf |
  - 9.1.10. Lysozyme as an example (pp. 189-190) | html | pdf |
  - 9.1.11. Rotation method: qualitative factors (pp. 190-191) | html | pdf |
  - 9.1.12. Radiation damage (pp. 191-192) | html | pdf |
  - 9.1.13. Relating data collection to the problem in hand (pp. 192-194) | html | pdf |
  - 9.1.14. The importance of low-resolution data (p. 194) | html | pdf |
  - 9.1.15. Data quality over the whole resolution range (p. 194) | html | pdf |
  - 9.1.16. Final remarks (pp. 194-195) | html | pdf |
  - References | html | pdf |

Part 10. Cryocrystallography
- 10.1. Introduction to cryocrystallography (pp. 197-201) | html | pdf | chapter contents |
  H. Hope
  - 10.1.1. Utility of low-temperature data collection (p. 197) | html | pdf |
  - 10.1.2. Cooling of biocrystals (pp. 197-199) | html | pdf |
  - 10.1.3. Principles of cooling equipment (p. 199) | html | pdf |
  - 10.1.4. Operational considerations (pp. 199-201) | html | pdf |
  - 10.1.5. Concluding note (p. 201) | html | pdf |
  - References | html | pdf |
- 10.2. Cryocrystallography techniques and devices (pp. 202-208) | html | pdf | chapter contents |
  D. W. Rodgers
  - 10.2.1. Introduction (p. 202) | html | pdf |
  - 10.2.2. Crystal preparation (pp. 202-203) | html | pdf |
  - 10.2.3. Crystal mounting (pp. 203-204) | html | pdf |
  - 10.2.4. Flash cooling (pp. 205-206) | html | pdf |
  - 10.2.5. Transfer and storage (pp. 206-207) | html | pdf |
  - References | html | pdf |

Part 11. Data processing
- 11.1. Automatic indexing of oscillation images (pp. 209-211) | html | pdf | chapter contents |
  M. G. Rossmann
  - 11.1.1. Introduction (p. 209) | html | pdf |
  - 11.1.2. The crystal orientation matrix (p. 209) | html | pdf |
  - 11.1.3. Fourier analysis of the reciprocal-lattice vector distribution when projected onto a chosen direction (pp. 209-210) | html | pdf |
  - 11.1.4. Exploring all possible directions to find a good set of basis vectors (p. 210) | html | pdf |
  - 11.1.5. The program (p. 211) | html | pdf |
  - References | html | pdf |
- 11.2. Integration of macromolecular diffraction data (pp. 212-217) | html | pdf | chapter contents |
  A. G. W. Leslie
  - 11.2.1. Introduction (p. 212) | html | pdf |
  - 11.2.2. Prerequisites for accurate integration (p. 212) | html | pdf |
  - 11.2.3. Methods of integration (p. 212) | html | pdf |
  - 11.2.4. The measurement box (pp. 212-213) | html | pdf |
  - 11.2.5. Integration by simple summation (pp. 213-214) | html | pdf |
  - 11.2.6. Integration by profile fitting (pp. 214-217) | html | pdf |
  - References | html | pdf |
- 11.3. Integration, scaling, space-group assignment and post refinement (pp. 218-225) | html | pdf | chapter contents |
  W. Kabsch
  - 11.3.1. Introduction (p. 218) | html | pdf |
  - 11.3.2. Modelling rotation images (pp. 218-221) | html | pdf |
  - 11.3.3. Integration (pp. 221-222) | html | pdf |
  - 11.3.4. Scaling (pp. 222-223) | html | pdf |
  - 11.3.5. Post refinement (pp. 223-224) | html | pdf |
  - 11.3.6. Space-group assignment (pp. 224-225) | html | pdf |
  - References | html | pdf |
- 11.4. DENZO and SCALEPACK (pp. 226-235) | html | pdf | chapter contents |
  Z. Otwinowski and W. Minor
  - 11.4.1. Introduction (p. 226) | html | pdf |
  - 11.4.2. Diffraction from a perfect crystal lattice (pp. 226-227) | html | pdf |
  - 11.4.3. Autoindexing (pp. 227-228) | html | pdf |
  - 11.4.4. Coordinate systems (pp. 228-229) | html | pdf |
  - 11.4.5. Experimental assumptions (pp. 229-231) | html | pdf |
  - 11.4.6. Prediction of the diffraction pattern (pp. 231-232) | html | pdf |
  - 11.4.7. Detector diagnostics (p. 233) | html | pdf |
  - 11.4.8. Multiplicative corrections (scaling) (p. 233) | html | pdf |
  - 11.4.9. Global refinement or post refinement (p. 233) | html | pdf |
  - 11.4.10. Graphical command centre (pp. 233-235) | html | pdf |
  - 11.4.11. Final note (p. 235) | html | pdf |
  - References | html | pdf |
- 11.5. The use of partially recorded reflections for post refinement, scaling and averaging X-ray diffraction data (pp. 236-245) | html | pdf | chapter contents |
  C. G. van Beek, R. Bolotovsky and M. G. Rossmann
  - 11.5.1. Introduction (p. 236) | html | pdf |
  - 11.5.2. Generalization of the Hamilton, Rollett and Sparks equations to take into account partial reflections (pp. 236-237) | html | pdf |
  - 11.5.3. Selection of reflections useful for scaling (p. 237) | html | pdf |
  - 11.5.4. Restraints and constraints (p. 237) | html | pdf |
  - 11.5.5. Generalization of the procedure for averaging reflection intensities (p. 238) | html | pdf |
  - 11.5.6. Estimating the quality of data scaling and averaging (p. 238) | html | pdf |
  - 11.5.7. Experimental results (pp. 238-241) | html | pdf |
  - 11.5.8. Conclusions (p. 241) | html | pdf |
  - Appendix 11.5.1. Partiality model (Rossmann, 1979; Rossmann et al. , 1979) (pp. 241-242) | html | pdf |
  - References | html | pdf |

Part 12. Isomorphous replacement
- 12.1. The preparation of heavy-atom derivatives of protein crystals for use in multiple isomorphous replacement and anomalous scattering (pp. 247-255) | html | pdf | chapter contents |
  D. Carvin, S. A. Islam,

International Tables for CrystallographyVolume F: Crystallography of biological macromolecules

Edited by M. G. Rossmann and E. Arnold

Contents

International Tables for Crystallography
Volume F: Crystallography of biological macromolecules