International Tables for Crystallography
Volume F: Crystallography of biological macromolecules

First online edition (2006)   ISBN: 978-0-7923-6857-1   doi: 10.1107/97809553602060000106     | 1 | 2 |

Edited by M. G. Rossmann and E. Arnold

Contents

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

• 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

• 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 |

• 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 |

• 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 |

• 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 |

• 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 |

• 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 |

• 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 |

• 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 |

• 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 |

• 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 |

• 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, M. J. E. Sternberg and T. L. Blundell
    • 12.1.1. Introduction  (p. 247) | html | pdf |
    • 12.1.2. Heavy-atom data bank  (pp. 247-248) | html | pdf |
    • 12.1.3. Properties of heavy-atom compounds and their complexes  (pp. 248-250) | html | pdf |
    • 12.1.4. Amino acids as ligands  (p. 250) | html | pdf |
    • 12.1.5. Protein chemistry of heavy-atom reagents  (pp. 250-254) | html | pdf |
    • 12.1.6. Metal-ion replacement in metalloproteins  (pp. 254-255) | html | pdf |
    • 12.1.7. Analogues of amino acids  (p. 255) | html | pdf |
    • 12.1.8. Use of the heavy-atom data bank to select derivatives  (p. 255) | html | pdf |
    • References | html | pdf |
  • 12.2. Locating heavy-atom sites  (pp. 256-262) | html | pdf | chapter contents |
    M. T. Stubbs and R. Huber
    • 12.2.1. The origin of the phase problem  (pp. 256-257) | html | pdf |
    • 12.2.2. The Patterson function  (pp. 257-258) | html | pdf |
    • 12.2.3. The difference Fourier  (p. 258) | html | pdf |
    • 12.2.4. Reality  (pp. 258-259) | html | pdf |
    • 12.2.5. Special complications   (pp. 259-260) | html | pdf |
    • References | html | pdf |

• Molecular replacement
  • 13.1. Noncrystallographic symmetry  (pp. 263-268) | html | pdf | chapter contents |
    D. M. Blow
    • 13.1.1. Introduction  (p. 263) | html | pdf |
    • 13.1.2. Definition of noncrystallographic symmetry  (p. 263) | html | pdf |
    • 13.1.3. Use of the Patterson function to interpret noncrystallographic symmetry  (pp. 263-265) | html | pdf |
    • 13.1.4. Interpretation of generalized noncrystallographic symmetry where the molecular structure is partially known  (pp. 265-266) | html | pdf |
    • 13.1.5. The power of noncrystallographic symmetry in structure analysis  (pp. 266-268) | html | pdf |
    • References | html | pdf |
  • 13.2. Rotation functions  (pp. 269-274) | html | pdf | chapter contents |
    J. Navaza
    • 13.2.1. Overview  (p. 269) | html | pdf |
    • 13.2.2. Rotations in three-dimensional Euclidean space  (pp. 269-270) | html | pdf |
    • 13.2.3. The rotation function  (pp. 270-272) | html | pdf |
    • 13.2.4. The locked rotation function  (pp. 272-273) | html | pdf |
    • 13.2.5. Other rotation functions  (p. 273) | html | pdf |
    • 13.2.6. Concluding remarks  (p. 273) | html | pdf |
    • Appendix 13.2.1. Formulae for the derivation and computation of the fast rotation function  (pp. 273-274) | html | pdf |
    • References | html | pdf |
  • 13.3. Translation functions  (pp. 275-278) | html | pdf | chapter contents |
    L. Tong
    • 13.3.1. Introduction  (p. 275) | html | pdf |
    • 13.3.2. R-factor and correlation-coefficient translation functions  (pp. 275-276) | html | pdf |
    • 13.3.3. Patterson-correlation translation function  (p. 276) | html | pdf |
    • 13.3.4. Phased translation function  (pp. 276-277) | html | pdf |
    • 13.3.5. Packing check in translation functions  (p. 277) | html | pdf |
    • 13.3.6. The unique region of a translation function (the Cheshire group)  (p. 277) | html | pdf |
    • 13.3.7. Combined molecular replacement  (p. 277) | html | pdf |
    • 13.3.8. The locked translation function  (pp. 277-278) | html | pdf |
    • 13.3.9. Miscellaneous translation functions  (p. 278) | html | pdf |
    • References | html | pdf |
  • 13.4. Noncrystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension  (pp. 279-292) | html | pdf | chapter contents |
    M. G. Rossmann and E. Arnold
    • 13.4.1. Introduction  (p. 279) | html | pdf |
    • 13.4.2. Noncrystallographic symmetry (NCS)  (pp. 279-280) | html | pdf |
    • 13.4.3. Phase determination using NCS  (pp. 280-281) | html | pdf |
    • 13.4.4. The p- and h-cells  (pp. 281-282) | html | pdf |
    • 13.4.5. Combining crystallographic and noncrystallographic symmetry  (pp. 282-283) | html | pdf |
    • 13.4.6. Determining the molecular envelope  (pp. 283-284) | html | pdf |
    • 13.4.7. Finding the averaged density  (pp. 284-285) | html | pdf |
    • 13.4.8. Interpolation  (p. 285) | html | pdf |
    • 13.4.9. Combining different crystal forms  (p. 285) | html | pdf |
    • 13.4.10. Phase extension and refinement of the NCS parameters  (pp. 285-286) | html | pdf |
    • 13.4.11. Convergence  (p. 286) | html | pdf |
    • 13.4.12. Ab initio phasing starts  (pp. 286-287) | html | pdf |
    • 13.4.13. Recent salient examples in low-symmetry cases: multidomain averaging and systematic applications of multiple-crystal-form averaging   (pp. 287-288) | html | pdf |
    • 13.4.14. Programs  (p. 288) | html | pdf |
    • References | html | pdf |

• Anomalous dispersion
  • 14.1. Heavy-atom location and phase determination with single-wavelength diffraction data  (pp. 293-298) | html | pdf | chapter contents |
    B. W. Matthews
    • 14.1.1. Introduction  (p. 293) | html | pdf |
    • 14.1.2. The isomorphous-replacement method  (pp. 293-294) | html | pdf |
    • 14.1.3. The method of multiple isomorphous replacement  (p. 294) | html | pdf |
    • 14.1.4. The method of Blow & Crick  (pp. 294-295) | html | pdf |
    • 14.1.5. The best Fourier  (p. 295) | html | pdf |
    • 14.1.6. Anomalous scattering  (p. 295) | html | pdf |
    • 14.1.7. Theory of anomalous scattering  (pp. 295-296) | html | pdf |
    • 14.1.8. The phase probability distribution for anomalous scattering  (p. 296) | html | pdf |
    • 14.1.9. Anomalous scattering without isomorphous replacement  (p. 297) | html | pdf |
    • 14.1.10. Location of heavy-atom sites  (p. 297) | html | pdf |
    • 14.1.11. Use of anomalous-scattering data in heavy-atom location  (p. 297) | html | pdf |
    • 14.1.12. Use of difference Fourier syntheses  (p. 297) | html | pdf |
    • 14.1.13. Single isomorphous replacement  (pp. 297-298) | html | pdf |
    • References | html | pdf |
  • 14.2. MAD and MIR  (pp. 299-309) | html | pdf | chapter contents |
    J. L. Smith, W. A. Hendrickson, T. C. Terwilliger and J. Berendzen
    • 14.2.1. Multiwavelength anomalous diffraction  (pp. 299-303) | html | pdf |
      J. L. Smith and W. A. Hendrickson
    • 14.2.2. Automated MAD and MIR structure solution  (pp. 303-307) | html | pdf |
      T. C. Terwilliger and J. Berendzen
    • References | html | pdf |

• Density modification and phase combination
  • 15.1. Phase improvement by iterative density modification  (pp. 311-324) | html | pdf | chapter contents |
    K. Y. J. Zhang, K. D. Cowtan and P. Main
    • 15.1.1. Introduction  (p. 311) | html | pdf |
    • 15.1.2. Density-modification methods  (pp. 311-318) | html | pdf |
    • 15.1.3. Reciprocal-space interpretation of density modification  (p. 319) | html | pdf |
    • 15.1.4. Phase combination  (pp. 319-321) | html | pdf |
    • 15.1.5. Combining constraints for phase improvement  (pp. 321-323) | html | pdf |
    • 15.1.6. Example  (pp. 323-324) | html | pdf |
    • References | html | pdf |
  • 15.2. Model phases: probabilities, bias and maps  (pp. 325-331) | html | pdf | chapter contents |
    R. J. Read
    • 15.2.1. Introduction  (p. 325) | html | pdf |
    • 15.2.2. Model bias: importance of phase  (p. 325) | html | pdf |
    • 15.2.3. Structure-factor probability relationships  (pp. 325-327) | html | pdf |
    • 15.2.4. Figure-of-merit weighting for model phases  (p. 327) | html | pdf |
    • 15.2.5. Map coefficients to reduce model bias  (pp. 327-328) | html | pdf |
    • 15.2.6. Estimation of overall coordinate error  (p. 328) | html | pdf |
    • 15.2.7. Difference-map coefficients  (p. 328) | html | pdf |
    • 15.2.8. Refinement bias  (pp. 328-329) | html | pdf |
    • 15.2.9. Maximum-likelihood structure refinement  (p. 329) | html | pdf |
    • References | html | pdf |

• Direct methods
  • 16.1. Ab initio phasing  (pp. 333-345) | html | pdf | chapter contents |
    G. M. Sheldrick, H. A. Hauptman, C. M. Weeks, R. Miller and I. Usón
    • 16.1.1. Introduction  (p. 333) | html | pdf |
    • 16.1.2. Normalized structure-factor magnitudes  (pp. 333-334) | html | pdf |
    • 16.1.3. Starting the phasing process  (pp. 334-335) | html | pdf |
    • 16.1.4. Reciprocal-space phase refinement or expansion (shaking)  (pp. 335-336) | html | pdf |
    • 16.1.5. Real-space constraints (baking)  (p. 336) | html | pdf |
    • 16.1.6. Fourier refinement (twice baking)  (pp. 336-337) | html | pdf |
    • 16.1.7. Computer programs for dual-space phasing  (pp. 337-339) | html | pdf |
    • 16.1.8. Applying dual-space programs successfully  (pp. 339-344) | html | pdf |
    • 16.1.9. Extending the power of direct methods  (pp. 344-345) | html | pdf |
    • References | html | pdf |
  • 16.2. The maximum-entropy method  (pp. 346-351) | html | pdf | chapter contents |
    G. Bricogne
    • 16.2.1. Introduction  (p. 346) | html | pdf |
    • 16.2.2. The maximum-entropy principle in a general context  (pp. 346-348) | html | pdf |
    • 16.2.3. Adaptation to crystallography  (p. 348) | html | pdf |
    • References | html | pdf |

• Model building and computer graphics
  • 17.1. Around O  (pp. 353-356) | html | pdf | chapter contents |
    G. J. Kleywegt, J.-Y. Zou, M. Kjeldgaard and T. A. Jones
    • 17.1.1. Introduction  (p. 353) | html | pdf |
    • 17.1.2. O  (pp. 353-354) | html | pdf |
    • 17.1.3. RAVE   (pp. 354-355) | html | pdf |
    • 17.1.4. Structure analysis  (p. 355) | html | pdf |
    • 17.1.5. Utilities  (pp. 355-356) | html | pdf |
    • 17.1.6. Other services  (p. 356) | html | pdf |
    • References | html | pdf |
  • 17.2. Molecular graphics and animation  (pp. 357-368) | html | pdf | chapter contents |
    A. J. Olson
    • 17.2.1. Introduction  (p. 357) | html | pdf |
    • 17.2.2. Background – the evolution of molecular graphics hardware and software   (pp. 357-358) | html | pdf |
    • 17.2.3. Representation and visualization of molecular data and models  (pp. 358-363) | html | pdf |
    • 17.2.4. Presentation graphics  (pp. 363-365) | html | pdf |
    • 17.2.5. Looking ahead  (pp. 365-366) | html | pdf |
    • References | html | pdf |

• Refinement
  • 18.1. Introduction to refinement  (pp. 369-374) | html | pdf | chapter contents |
    L. F. Ten Eyck and K. D. Watenpaugh
    • 18.1.1. Overview  (p. 369) | html | pdf |
    • 18.1.2. Background  (p. 369) | html | pdf |
    • 18.1.3. Objectives  (p. 369) | html | pdf |
    • 18.1.4. Least squares and maximum likelihood  (pp. 369-370) | html | pdf |
    • 18.1.5. Optimization  (p. 370) | html | pdf |
    • 18.1.6. Data  (p. 370) | html | pdf |
    • 18.1.7. Models  (pp. 370-372) | html | pdf |
    • 18.1.8. Optimization methods  (pp. 372-373) | html | pdf |
    • 18.1.9. Evaluation of the model  (pp. 373-374) | html | pdf |
    • 18.1.10. Conclusion  (p. 374) | html | pdf |
    • References | html | pdf |
  • 18.2. Enhanced macromolecular refinement by simulated annealing  (pp. 375-381) | html | pdf | chapter contents |
    A. T. Brunger, P. D. Adams and L. M. Rice
    • 18.2.1. Introduction  (p. 375) | html | pdf |
    • 18.2.2. Cross validation  (p. 375) | html | pdf |
    • 18.2.3. The target function  (pp. 375-377) | html | pdf |
    • 18.2.4. Searching conformational space  (pp. 377-379) | html | pdf |
    • 18.2.5. Examples  (pp. 379-380) | html | pdf |
    • 18.2.6. Multi-start refinement and structure-factor averaging  (p. 380) | html | pdf |
    • 18.2.7. Ensemble models  (p. 380) | html | pdf |
    • 18.2.8. Conclusions  (p. 381) | html | pdf |
    • References | html | pdf |
  • 18.3. Structure quality and target parameters  (pp. 382-392) | html | pdf | chapter contents |
    R. A. Engh and R. Huber
    • 18.3.1. Purpose of restraints  (p. 382) | html | pdf |
    • 18.3.2. Formulation of refinement restraints  (pp. 382-392) | html | pdf |
    • 18.3.3. Strategy of application during building/refinement  (p. 392) | html | pdf |
    • 18.3.4. Future perspectives  (p. 392) | html | pdf |
    • References | html | pdf |
  • 18.4. Refinement at atomic resolution  (pp. 393-402) | html | pdf | chapter contents |
    Z. Dauter, G. N. Murshudov and K. S. Wilson
    • 18.4.1. Definition of atomic resolution  (pp. 393-395) | html | pdf |
    • 18.4.2. Data  (p. 395) | html | pdf |
    • 18.4.3. Computational algorithms and strategies  (p. 396) | html | pdf |
    • 18.4.4. Computational options and tactics  (pp. 396-398) | html | pdf |
    • 18.4.5. Features in the refined model  (pp. 398-401) | html | pdf |
    • 18.4.6. Quality assessment of the model  (p. 401) | html | pdf |
    • 18.4.7. Relation to biological chemistry   (pp. 401-402) | html | pdf |
    • References | html | pdf |
  • 18.5. Coordinate uncertainty  (pp. 403-418) | html | pdf | chapter contents |
    D. W. J. Cruickshank
    • 18.5.1. Introduction  (p. 403) | html | pdf |
    • 18.5.2. The least-squares method  (pp. 404-405) | html | pdf |
    • 18.5.3. Restrained refinement  (pp. 405-406) | html | pdf |
    • 18.5.4. Two examples of full-matrix inversion  (pp. 406-409) | html | pdf |
    • 18.5.5. Approximate methods  (p. 409) | html | pdf |
    • 18.5.6. The diffraction-component precision index  (p. 410) | html | pdf |
    • 18.5.7. Examples of the diffraction-component precision index  (pp. 411-412) | html | pdf |
    • 18.5.8. Luzzati plots  (pp. 412-414) | html | pdf |
    • References | html | pdf |

• Other experimental techniques
  • 19.1. Neutron crystallography: methods and information content  (pp. 419-422) | html | pdf | chapter contents |
    A. A. Kossiakoff
    • 19.1.1. Introduction  (p. 419) | html | pdf |
    • 19.1.2. Diffraction geometries  (p. 419) | html | pdf |
    • 19.1.3. Neutron density maps – information content  (pp. 419-420) | html | pdf |
    • 19.1.4. Phasing models and evaluation of correctness  (p. 420) | html | pdf |
    • 19.1.5. Evaluation of correctness  (pp. 420-421) | html | pdf |
    • 19.1.6. Refinement  (p. 421) | html | pdf |
    • 19.1.7. D₂O − H₂O solvent difference maps  (pp. 421-422) | html | pdf |
    • 19.1.8. Applications of D₂O − H₂O solvent difference maps  (p. 422) | html | pdf |
    • References | html | pdf |
  • 19.2. Electron diffraction of protein crystals  (pp. 423-427) | html | pdf | chapter contents |
    W. Chiu
    • 19.2.1. Electron scattering  (p. 423) | html | pdf |
    • 19.2.2. The electron microscope  (p. 423) | html | pdf |
    • 19.2.3. Data collection  (pp. 423-424) | html | pdf |
    • 19.2.4. Data processing  (pp. 425-427) | html | pdf |
    • 19.2.5. Future development  (p. 427) | html | pdf |
    • References | html | pdf |
  • 19.3. Small-angle X-ray scattering  (pp. 428-437) | html | pdf | chapter contents |
    H. Tsuruta and J. E. Johnson
    • 19.3.1. Introduction  (p. 428) | html | pdf |
    • 19.3.2. Small-angle single-crystal X-ray diffraction studies  (pp. 428-429) | html | pdf |
    • 19.3.3. Solution X-ray scattering studies  (pp. 429-437) | html | pdf |
    • References | html | pdf |
  • 19.4. Small-angle neutron scattering  (pp. 438-443) | html | pdf | chapter contents |
    D. M. Engelman and P. B. Moore
    • 19.4.1. Introduction  (p. 438) | html | pdf |
    • 19.4.2. Fundamental relationships  (pp. 438-439) | html | pdf |
    • 19.4.3. Contrast variation  (pp. 439-441) | html | pdf |
    • 19.4.4. Distance measurements  (p. 442) | html | pdf |
    • 19.4.5. Practical considerations  (pp. 442-443) | html | pdf |
    • 19.4.6. Examples  (p. 443) | html | pdf |
    • References | html | pdf |
  • 19.5. Fibre diffraction  (pp. 444-450) | html | pdf | chapter contents |
    R. Chandrasekaran and G. Stubbs
    • 19.5.1. Introduction  (p. 444) | html | pdf |
    • 19.5.2. Types of fibres  (pp. 444-445) | html | pdf |
    • 19.5.3. Diffraction by helical molecules  (pp. 445-446) | html | pdf |
    • 19.5.4. Fibre preparation  (p. 446) | html | pdf |
    • 19.5.5. Data collection  (p. 446) | html | pdf |
    • 19.5.6. Data processing  (pp. 446-447) | html | pdf |
    • 19.5.7. Determination of structures  (pp. 447-449) | html | pdf |
    • 19.5.8. Structures determined by X-ray fibre diffraction  (pp. 449-450) | html | pdf |
    • References | html | pdf |
  • 19.6. Electron cryomicroscopy  (pp. 451-463) | html | pdf | chapter contents |
    T. S. Baker and R. Henderson
    • 19.6.1. Abbreviations used  (p. 451) | html | pdf |
    • 19.6.2. The role of electron microscopy in macromolecular structure determination  (pp. 451-452) | html | pdf |
    • 19.6.3. Electron scattering and radiation damage  (pp. 452-453) | html | pdf |
    • 19.6.4. Three-dimensional electron cryomicroscopy of macromolecules  (pp. 453-463) | html | pdf |
    • 19.6.5. Recent trends  (p. 463) | html | pdf |
    • References | html | pdf |
  • 19.7. Nuclear magnetic resonance (NMR) spectroscopy  (pp. 464-479) | html | pdf | chapter contents |
    K. Wüthrich
    • 19.7.1. Complementary roles of NMR in solution and X-ray crystallography in structural biology  (p. 464) | html | pdf |
    • 19.7.2. A standard protocol for NMR structure determination of proteins and nucleic acids  (pp. 464-466) | html | pdf |
    • 19.7.3. Combined use of single-crystal X-ray diffraction and solution NMR for structure determination  (p. 466) | html | pdf |
    • 19.7.4. NMR studies of solvation in solution  (p. 466) | html | pdf |
    • 19.7.5. NMR studies of rate processes and conformational equilibria in three-dimensional macromolecular structures  (pp. 466-467) | html | pdf |
    • References | html | pdf |

• Energy calculations and molecular dynamics
  • 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin  (pp. 481-488) | html | pdf | chapter contents |
    U. Stocker and W. F. van Gunsteren
    • 20.1.1. Introduction  (p. 481) | html | pdf |
    • 20.1.2. Methods  (pp. 481-482) | html | pdf |
    • 20.1.3. Results  (pp. 482-488) | html | pdf |
    • 20.1.4. Conclusions  (p. 488) | html | pdf |
    • References | html | pdf |
  • 20.2. Molecular-dynamics simulations of biological macromolecules  (pp. 489-495) | html | pdf | chapter contents |
    C. B. Post and V. M. Dadarlat
    • 20.2.1. Introduction  (p. 489) | html | pdf |
    • 20.2.2. The simulation method  (p. 489) | html | pdf |
    • 20.2.3. Potential-energy function  (pp. 489-491) | html | pdf |
    • 20.2.4. Empirical parameterization of the force field  (p. 491) | html | pdf |
    • 20.2.5. Modifications in the force field for structure determination  (p. 491) | html | pdf |
    • 20.2.6. Internal dynamics and average structures  (p. 491) | html | pdf |
    • 20.2.7. Assessment of the simulation procedure  (p. 492) | html | pdf |
    • 20.2.8. Effect of crystallographic atomic resolution on structural stability during molecular dynamics  (pp. 492-494) | html | pdf |
    • References | html | pdf |

• Structure validation
  • 21.1. Validation of protein crystal structures  (pp. 497-506) | html | pdf | chapter contents |
    G. J. Kleywegt
    • 21.1.1. Introduction  (p. 497) | html | pdf |
    • 21.1.2. Types of error  (pp. 497-498) | html | pdf |
    • 21.1.3. Detecting outliers  (pp. 498-499) | html | pdf |
    • 21.1.4. Fixing errors  (p. 499) | html | pdf |
    • 21.1.5. Preventing errors  (pp. 499-500) | html | pdf |
    • 21.1.6. Final model  (p. 500) | html | pdf |
    • 21.1.7. A compendium of quality criteria  (pp. 500-505) | html | pdf |
    • 21.1.8. Future  (p. 506) | html | pdf |
    • References | html | pdf |
  • 21.2. Assessing the quality of macromolecular structures  (pp. 507-519) | html | pdf | chapter contents |
    S. J. Wodak, A. A. Vagin, J. Richelle, U. Das, J. Pontius and H. M. Berman
    • 21.2.1. Introduction  (p. 507) | html | pdf |
    • 21.2.2. Validating the geometric and stereochemical parameters of the model  (pp. 507-509) | html | pdf |
    • 21.2.3. Validation of a model versus experimental data  (pp. 509-517) | html | pdf |
    • 21.2.4. Atomic resolution structures  (pp. 517-518) | html | pdf |
    • 21.2.5. Concluding remarks  (p. 518) | html | pdf |
    • References | html | pdf |
  • 21.3. Detection of errors in protein models  (pp. 520-530) | html | pdf | chapter contents |
    O. Dym, D. Eisenberg and T. O. Yeates
    • 21.3.1. Motivation and introduction  (p. 520) | html | pdf |
    • 21.3.2. Separating evaluation from refinement  (p. 520) | html | pdf |
    • 21.3.3. Algorithms for the detection of errors in protein models and the types of errors they detect  (pp. 520-521) | html | pdf |
    • 21.3.4. Selection of database  (p. 521) | html | pdf |
    • 21.3.5. Examples: detection of errors in structures  (pp. 521-525) | html | pdf |
    • 21.3.6. Summary  (p. 525) | html | pdf |
    • 21.3.7. Availability of software  (p. 525) | html | pdf |
    • References | html | pdf |

• Molecular geometry and features
  • 22.1. Protein surfaces and volumes: measurement and use  (pp. 531-545) | html | pdf | chapter contents |
    M. Gerstein, F. M. Richards, M. S. Chapman and M. L. Connolly
    • 22.1.1. Protein geometry: volumes, areas and distances  (pp. 531-539) | html | pdf |
      M. Gerstein and F. M. Richards
    • 22.1.2. Molecular surfaces: calculations, uses and representations  (pp. 539-545) | html | pdf |
      M. S. Chapman and M. L. Connolly
    • References | html | pdf |
  • 22.2. Hydrogen bonding in biological macromolecules  (pp. 546-552) | html | pdf | chapter contents |
    E. N. Baker
    • 22.2.1. Introduction  (p. 546) | html | pdf |
    • 22.2.2. Nature of the hydrogen bond  (p. 546) | html | pdf |
    • 22.2.3. Hydrogen-bonding groups  (pp. 546-547) | html | pdf |
    • 22.2.4. Identification of hydrogen bonds: geometrical considerations  (p. 547) | html | pdf |
    • 22.2.5. Hydrogen bonding in proteins  (pp. 547-551) | html | pdf |
    • 22.2.6. Hydrogen bonding in nucleic acids  (p. 551) | html | pdf |
    • 22.2.7. Non-conventional hydrogen bonds  (pp. 551-552) | html | pdf |
    • References | html | pdf |
  • 22.3. Electrostatic interactions in proteins  (pp. 553-557) | html | pdf | chapter contents |
    K. A. Sharp
    • 22.3.1. Introduction  (p. 553) | html | pdf |
    • 22.3.2. Theory  (pp. 553-555) | html | pdf |
    • 22.3.3. Applications  (pp. 555-556) | html | pdf |
    • References | html | pdf |
  • 22.4. The relevance of the Cambridge Structural Database in protein crystallography  (pp. 558-574) | html | pdf | chapter contents |
    F. H. Allen, J. C. Cole and M. L. Verdonk
    • 22.4.1. Introduction  (p. 558) | html | pdf |
    • 22.4.2. The CSD and the PDB: data acquisition and data quality  (pp. 558-559) | html | pdf |
    • 22.4.3. Structural knowledge from the CSD  (pp. 559-560) | html | pdf |
    • 22.4.4. Intramolecular geometry  (pp. 560-562) | html | pdf |
    • 22.4.5. Intermolecular data  (pp. 562-567) | html | pdf |
    • 22.4.6. Conclusion  (p. 567) | html | pdf |
    • References | html | pdf |

• Structural analysis and classification
  • 23.1. Protein folds and motifs: representation, comparison and classification  (pp. 575-578) | html | pdf | chapter contents |
    C. Orengo, J. Thornton, L. Holm and C. Sander
    • 23.1.1. Protein-fold classification  (pp. 575-576) | html | pdf |
      C. Orengo and J. Thornton
    • 23.1.2. Locating domains in 3D structures  (pp. 577-578) | html | pdf |
      L. Holm and C. Sander
    • References | html | pdf |
  • 23.2. Protein–ligand interactions  (pp. 579-587) | html | pdf | chapter contents |
    A. E. Hodel and F. A. Quiocho
    • 23.2.1. Introduction  (p. 579) | html | pdf |
    • 23.2.2. Protein–carbohydrate interactions  (pp. 579-580) | html | pdf |
    • 23.2.3. Metals  (pp. 580-581) | html | pdf |
    • 23.2.4. Protein–nucleic acid interactions  (pp. 581-585) | html | pdf |
    • 23.2.5. Phosphate and sulfate  (pp. 585-587) | html | pdf |
    • References | html | pdf |
  • 23.3. Nucleic acids  (pp. 588-622) | html | pdf | chapter contents |
    R. E. Dickerson
    • 23.3.1. Introduction  (p. 588) | html | pdf |
    • 23.3.2. Helix parameters  (pp. 588-596) | html | pdf |
    • 23.3.3. Comparison of A, B and Z helices  (pp. 596-602) | html | pdf |
    • 23.3.4. Sequence–structure relationships in B-DNA  (pp. 602-609) | html | pdf |
    • 23.3.5. Summary  (p. 609) | html | pdf |
    • Appendix 23.3.1. X-ray analyses of A, B and Z helices  (pp. 609-622) | html | pdf |
    • References | html | pdf |
  • 23.4. Solvent structure  (pp. 623-647) | html | pdf | chapter contents |
    C. Mattos and D. Ringe
    • 23.4.1. Introduction  (pp. 623-624) | html | pdf |
    • 23.4.2. Determination of water molecules  (pp. 624-625) | html | pdf |
    • 23.4.3. Structural features of protein–water interactions derived from database analysis  (pp. 625-630) | html | pdf |
    • 23.4.4. Water structure in groups of well studied proteins  (pp. 630-637) | html | pdf |
    • 23.4.5. The classic models: small proteins with high-resolution crystal structures  (pp. 637-638) | html | pdf |
    • 23.4.6. Water molecules as mediators of complex formation  (pp. 638-640) | html | pdf |
    • 23.4.7. Conclusions and future perspectives  (p. 640) | html | pdf |
    • References | html | pdf |

• Crystallographic databases
  • 24.1. The Protein Data Bank at Brookhaven  (pp. 649-656) | html | pdf | chapter contents |
    J. L. Sussman, D. Lin, J. Jiang, N. O. Manning, J. Prilusky and E. E. Abola
    • 24.1.1. Introduction  (p. 649) | html | pdf |
    • 24.1.2. Background and significance of the resource  (pp. 649-650) | html | pdf |
    • 24.1.3. The PDB in 1999  (pp. 650-654) | html | pdf |
    • 24.1.4. Examples of the impact of the PDB  (pp. 654-656) | html | pdf |
    • References | html | pdf |
  • 24.2. The Nucleic Acid Database (NDB)  (pp. 657-662) | html | pdf | chapter contents |
    H. M. Berman, Z. Feng, B. Schneider, J. Westbrook and C. Zardecki
    • 24.2.1. Introduction  (p. 657) | html | pdf |
    • 24.2.2. Information content of the NDB  (p. 657) | html | pdf |
    • 24.2.3. Data processing  (pp. 657-659) | html | pdf |
    • 24.2.4. The database  (p. 659) | html | pdf |
    • 24.2.5. Data distribution  (pp. 659-662) | html | pdf |
    • 24.2.6. Outreach  (p. 662) | html | pdf |
    • References | html | pdf |
  • 24.3. The Cambridge Structural Database (CSD)  (pp. 663-668) | html | pdf | chapter contents |
    F. H. Allen and V. J. Hoy
    • 24.3.1. Introduction and historical perspective  (p. 663) | html | pdf |
    • 24.3.2. Information content of the CSD  (pp. 663-665) | html | pdf |
    • 24.3.3. The CSD software system  (pp. 665-666) | html | pdf |
    • 24.3.4. Knowledge engineering from the CSD  (pp. 667-668) | html | pdf |
    • 24.3.5. Accessing the CSD system and IsoStar  (p. 668) | html | pdf |
    • 24.3.6. Conclusion  (p. 668) | html | pdf |
  • 24.4. The Biological Macromolecule Crystallization Database  (pp. 669-674) | html | pdf | chapter contents |
    G. L. Gilliland, M. Tung and J. E. Ladner
    • 24.4.1. Introduction  (p. 669) | html | pdf |
    • 24.4.2. History of the BMCD  (p. 669) | html | pdf |
    • 24.4.3. BMCD data  (p. 669) | html | pdf |
    • 24.4.4. BMCD implementation – web interface  (p. 670) | html | pdf |
    • 24.4.5. Reproducing published crystallization procedures  (pp. 670-671) | html | pdf |
    • 24.4.6. Crystallization screens  (p. 671) | html | pdf |
    • 24.4.7. A general crystallization procedure  (pp. 671-674) | html | pdf |
    • 24.4.8. The future of the BMCD  (p. 674) | html | pdf |
    • References | html | pdf |
  • 24.5. The Protein Data Bank, 1999–  (pp. 675-684) | html | pdf | chapter contents |
    H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne
    • 24.5.1. Introduction  (p. 675) | html | pdf |
    • 24.5.2. Data acquisition and processing  (pp. 675-677) | html | pdf |
    • 24.5.3. The PDB database resource  (pp. 677-678) | html | pdf |
    • 24.5.4. Data distribution  (p. 679) | html | pdf |
    • 24.5.5. Data archiving  (pp. 679-680) | html | pdf |
    • 24.5.6. Maintenance of the legacy of the BNL system  (p. 680) | html | pdf |
    • 24.5.7. Current developments  (p. 680) | html | pdf |
    • 24.5.8. PDB advisory boards  (p. 680) | html | pdf |
    • 24.5.9. Further information  (pp. 680-681) | html | pdf |
    • 24.5.10. Conclusion  (p. 681) | html | pdf |
    • References | html | pdf |

• Macromolecular crystallography programs
  • 25.1. Survey of programs for crystal structure determination and analysis of macromolecules  (pp. 685-694) | html | pdf | chapter contents |
    J. Ding and E. Arnold
    • 25.1.1. Introduction  (p. 685) | html | pdf |
    • 25.1.2. Multipurpose crystallographic program systems  (pp. 685-687) | html | pdf |
    • 25.1.3. Data collection and processing  (pp. 687-688) | html | pdf |
    • 25.1.4. Phase determination and structure solution  (pp. 688-689) | html | pdf |
    • 25.1.5. Structure refinement  (p. 689) | html | pdf |
    • 25.1.6. Phase improvement and density-map modification  (pp. 689-690) | html | pdf |
    • 25.1.7. Graphics and model building  (pp. 690-691) | html | pdf |
    • 25.1.8. Structure analysis and verification  (pp. 691-693) | html | pdf |
    • 25.1.9. Structure presentation  (pp. 693-694) | html | pdf |
    • References | html | pdf |
  • 25.2. Programs and program systems in wide use  (pp. 695-743) | html | pdf | chapter contents |
    W. Furey, K. D. Cowtan, K. Y. J. Zhang, P. Main, A. T. Brunger, P. D. Adams, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, D. E. Tronrud, L. F. Ten Eyck, V. S. Lamzin, A. Perrakis, K. S. Wilson, R. A. Laskowski, M. W. MacArthur, J. M. Thornton, P. J. Kraulis, D. C. Richardson, J. S. Richardson, W. Kabsch and G. M. Sheldrick
    • 25.2.1. PHASES  (pp. 695-705) | html | pdf |
      W. Furey
    • 25.2.2. DM/DMMULTI software for phase improvement by density modification  (pp. 705-710) | html | pdf |
      K. D. Cowtan, K. Y. J. Zhang and P. Main
    • 25.2.3. The structure-determination language of the Crystallography & NMR System  (pp. 710-716) | html | pdf |
      A. T. Brunger, P. D. Adams, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, N. S. Pannu, R. J. Read, L. M. Rice and T. Simonson
    • 25.2.4. The TNT refinement package  (pp. 716-720) | html | pdf |
      D. E. Tronrud and L. F. Ten Eyck
    • 25.2.5. The ARP/wARP suite for automated construction and refinement of protein models  (pp. 720-722) | html | pdf |
      V. S. Lamzin, A. Perrakis and K. S. Wilson
    • 25.2.6. PROCHECK: validation of protein-structure coordinates  (pp. 722-725) | html | pdf |
      R. A. Laskowski, M. W. MacArthur and J. M. Thornton
    • 25.2.7. MolScript  (pp. 725-727) | html | pdf |
      P. J. Kraulis
    • 25.2.8. MAGE, PROBE and kinemages  (pp. 727-730) | html | pdf |
      D. C. Richardson and J. S. Richardson
    • 25.2.9. XDS  (pp. 730-734) | html | pdf |
      W. Kabsch
    • 25.2.10. Macromolecular applications of SHELX  (pp. 734-738) | html | pdf |
      G. M. Sheldrick
    • References | html | pdf |

• A historical perspective
  • 26.1. How the structure of lysozyme was actually determined  (pp. 745-772) | html | pdf | chapter contents |
    C. C. F. Blake, R. H. Fenn, L. N. Johnson, D. F. Koenig, G. A. Mair, A. C. T. North, J. W. H. Oldham, D. C. Phillips, R. J. Poljak, V. R. Sarma and C. A. Vernon
    • 26.1.1. Introduction  (p. 745) | html | pdf |
    • 26.1.2. Structure analysis at 6 Å resolution  (pp. 745-753) | html | pdf |
    • 26.1.3. Analysis of the structure at 2 Å resolution  (pp. 753-765) | html | pdf |
    • 26.1.4. Structural studies on the biological function of lysozyme  (pp. 765-769) | html | pdf |
    • References | html | pdf |