International Tables for Crystallography
Volume F: Crystallography of biological macromolecules

Second online edition (2012)   ISBN: 978-0-470-66078-2   doi: 10.1107/97809553602060000111     | 1 | 2 |

Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

Contents

• Preface to the second edition  (p. xxix) | html | pdf |
  E. Arnold, D. M. Himmel and M. G. Rossmann

• Introduction
  • 1.1. Overview  (pp. 1-4) | html | pdf | chapter contents |
    E. Arnold, D. M. Himmel and M. G. Rossmann
  • 1.2. Historical background  (pp. 5-12) | html | pdf | chapter contents |
    M. G. Rossmann
    • 1.2.1. Introduction  (p. 5) | html | pdf |
    • 1.2.2. 1912 to the 1950s  (pp. 5-6) | html | pdf |
    • 1.2.3. The first investigations of biological macromolecules  (pp. 6-7) | html | pdf |
    • 1.2.4. Globular proteins in the 1950s  (pp. 7-8) | html | pdf |
    • 1.2.5. The first protein structures (1957 to the 1970s)  (pp. 8-9) | html | pdf |
    • 1.2.6. Technological developments (1958 to the 1980s)  (pp. 9-10) | html | pdf |
    • 1.2.7. Meetings  (p. 10) | html | pdf |
    • References | html | pdf |
  • 1.3. Macromolecular crystallography and medicine  (pp. 13-38) | html | pdf | chapter contents |
    W. G. J. Hol and C. L. M. J. Verlinde
    • 1.3.1. Introduction  (p. 13) | html | pdf |
    • 1.3.2. Crystallography and medicine  (pp. 13-14) | html | pdf |
    • 1.3.3. Crystallography and genetic diseases  (pp. 14-15) | html | pdf |
    • 1.3.4. Crystallography and development of novel pharmaceuticals  (pp. 15-26) | html | pdf |
    • 1.3.5. Vaccines, immunology and crystallography  (p. 26) | html | pdf |
    • 1.3.6. Outlook and dreams  (pp. 26-27) | html | pdf |
    • References | html | pdf |
  • 1.4. Perspectives for the future  (pp. 39-44) | html | pdf | chapter contents |
    E. Arnold, M. G. Rossmann, D. M. Himmel, J. C. H. Spence and S. Sun
    • 1.4.1. Gazing into the crystal ball (E. Arnold)  (pp. 39-40) | html | pdf |
    • 1.4.2. Brief comments on Gazing into the crystal ball (M. G. Rossmann)  (p. 40) | html | pdf |
    • 1.4.3. Additional comments on Gazing into the crystal ball (D. M. Himmel)  (p. 41) | html | pdf |
    • 1.4.4. Gazing into the crystal ball – the X-ray free-electron laser (J. C. H. Spence)  (pp. 41-42) | html | pdf |
    • 1.4.5. Electron microscopy's impact on structural biology (S. Sun)  (pp. 42-43) | html | pdf |
    • References | html | pdf |

• 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. 58-60) | html | pdf |
    • 2.1.7. Calculation of electron density  (p. 60) | html | pdf |
    • 2.1.8. Symmetry in the diffraction pattern  (pp. 60-61) | html | pdf |
    • 2.1.9. The Patterson function  (pp. 62-63) | html | pdf |
    • References | html | pdf |
  • 2.2. Quality indicators in macromolecular crystallography: definitions and applications  (pp. 64-74) | html | pdf | chapter contents |
    H. M. Einspahr and M. S. Weiss
    • 2.2.1. Introduction  (pp. 64-65) | html | pdf |
    • 2.2.2. Quality indicators for diffraction data  (pp. 65-68) | html | pdf |
    • 2.2.3. Comparing different diffraction data sets  (p. 68) | html | pdf |
    • 2.2.4. Quality indicators for substructure determination  (pp. 68-69) | html | pdf |
    • 2.2.5. Quality indicators for phase determination  (p. 69) | html | pdf |
    • 2.2.6. Quality indicators for density modification and phase improvement  (pp. 69-70) | html | pdf |
    • 2.2.7. Quality indicators for molecular replacement  (pp. 70-71) | html | pdf |
    • 2.2.8. Quality indicators for refinement  (p. 71) | html | pdf |
    • 2.2.9. Quality indicators for the refined model  (pp. 71-73) | html | pdf |
    • 2.2.10. Error estimation for the refined model  (p. 73) | html | pdf |
    • 2.2.11. The most commonly used quality indicators  (p. 73) | html | pdf |
    • References | html | pdf |

• Techniques of molecular biology
  • 3.1. Preparing recombinant proteins for X-ray crystallography  (pp. 75-91) | html | pdf | chapter contents |
    S. H. Hughes and A. M. Stock
    • 3.1.1. Introduction  (p. 75) | html | pdf |
    • 3.1.2. Overview  (pp. 75-76) | html | pdf |
    • 3.1.3. Engineering an expression construct  (pp. 76-77) | html | pdf |
    • 3.1.4. Expression systems  (pp. 77-85) | html | pdf |
    • 3.1.5. Protein purification  (pp. 85-88) | html | pdf |
    • 3.1.6. Characterization of the purified product  (pp. 88-89) | html | pdf |
    • 3.1.7. Reprise  (pp. 89-90) | html | pdf |
    • References | html | pdf |
  • 3.2. Expression and purification of membrane proteins for structural studies  (pp. 92-98) | html | pdf | chapter contents |
    J. A. Ernst, D. G. Yansura and C. M. Koth
    • 3.2.1. Introduction  (p. 92) | html | pdf |
    • 3.2.2. A consensus strategy for membrane-protein expression  (pp. 92-93) | html | pdf |
    • 3.2.3. A consensus strategy for membrane-protein purification  (pp. 93-96) | html | pdf |
    • 3.2.4. Common purification pitfalls and prioritized alternative strategies  (p. 96) | html | pdf |
    • 3.2.5. Summary  (p. 96) | html | pdf |
    • References | html | pdf |

• Crystallization
  • 4.1. General methods  (pp. 99-121) | html | pdf | chapter contents |
    C. Sauter, B. Lorber, A. McPherson and R. Giegé
    • 4.1.1. Introduction  (pp. 99-100) | html | pdf |
    • 4.1.2. Main parameters that affect crystallization of macromolecules  (pp. 100-104) | html | pdf |
    • 4.1.3. Crystallization arrangements and classical methodologies  (pp. 104-107) | html | pdf |
    • 4.1.4. Advanced crystallization methodologies  (pp. 107-111) | html | pdf |
    • 4.1.5. From the macromolecule to perfect crystals: the physics view  (pp. 111-113) | html | pdf |
    • 4.1.6. How to crystallize a new macromolecule: the structural biology view  (pp. 113-115) | html | pdf |
    • 4.1.7. The future of protein crystal growth  (p. 115) | html | pdf |
    • References | html | pdf |
  • 4.2. Crystallization of membrane proteins  (pp. 122-128) | html | pdf | chapter contents |
    H. Michel
    • 4.2.1. Introduction  (p. 122) | html | pdf |
    • 4.2.2. Principles of membrane-protein crystallization  (pp. 122-123) | html | pdf |
    • 4.2.3. General properties of detergents relevant to membrane-protein crystallization  (pp. 123-125) | html | pdf |
    • 4.2.4. The `small amphiphile concept'  (pp. 125-126) | html | pdf |
    • 4.2.5. Membrane-protein crystallization with the help of antibody Fv fragments  (p. 126) | html | pdf |
    • 4.2.6. Membrane-protein crystallization using cubic bicontinuous lipidic phases  (p. 126) | html | pdf |
    • 4.2.7. General recommendations  (pp. 126-127) | html | pdf |
    • References | html | pdf |
  • 4.3. Application of protein engineering to enhance crystallizability and improve crystal properties  (pp. 129-139) | html | pdf | chapter contents |
    Z. S. Derewenda
    • 4.3.1. Introduction  (p. 129) | html | pdf |
    • 4.3.2. Microscopic aspects of protein crystallization  (pp. 129-130) | html | pdf |
    • 4.3.3. Engineering proteins with enhanced solubility  (pp. 130-131) | html | pdf |
    • 4.3.4. Optimization of target constructs  (p. 131) | html | pdf |
    • 4.3.5. The use of fusion proteins for crystallization  (pp. 131-132) | html | pdf |
    • 4.3.6. Noncovalent crystallization chaperones  (pp. 132-133) | html | pdf |
    • 4.3.7. Removal of post-translational modifications  (pp. 133-134) | html | pdf |
    • 4.3.8. Stabilization of protein targets  (p. 134) | html | pdf |
    • 4.3.9. Surface-entropy reduction (SER)  (pp. 134-135) | html | pdf |
    • 4.3.10. Improvement of crystal quality  (p. 135) | html | pdf |
    • 4.3.11. Conclusions  (pp. 135-136) | html | pdf |
    • References | html | pdf |
  • 4.4. High-throughput X-ray crystallography   (pp. 140-144) | html | pdf | chapter contents |
    K. H. Choi
    • 4.4.1. Introduction  (p. 140) | html | pdf |
    • 4.4.2. Design of multiple constructs: bioinformatics analysis of genome sequences  (p. 140) | html | pdf |
    • 4.4.3. Cloning  (pp. 140-142) | html | pdf |
    • 4.4.4. Protein expression and purification  (p. 142) | html | pdf |
    • 4.4.5. Crystallization  (pp. 142-143) | html | pdf |
    • 4.4.6. Synchrotron data collection  (p. 143) | html | pdf |
    • References | html | pdf |

• Crystal properties and handling
  • 5.1. Crystal morphology, optical properties of crystals and crystal mounting  (pp. 145-151) | html | pdf | chapter contents |
    H. L. Carrell and J. P. Glusker
    • 5.1.1. Crystal morphology and optical properties  (pp. 145-148) | html | pdf |
    • 5.1.2. Crystal mounting  (pp. 148-150) | html | pdf |
    • References | html | pdf |
  • 5.2. Crystal-density measurements  (pp. 152-157) | html | pdf | chapter contents |
    E. M. Westbrook
    • 5.2.1. Introduction  (p. 152) | html | pdf |
    • 5.2.2. Solvent in macromolecular crystals  (p. 152) | html | pdf |
    • 5.2.3. Matthews number  (p. 152) | html | pdf |
    • 5.2.4. Algebraic concepts  (pp. 152-153) | html | pdf |
    • 5.2.5. Experimental estimation of hydration  (p. 153) | html | pdf |
    • 5.2.6. Methods for measuring crystal density  (pp. 153-156) | html | pdf |
    • 5.2.7. How to handle the solvent density  (p. 156) | html | pdf |
    • References | html | pdf |

• Radiation sources and optics
  • 6.1. X-ray sources  (pp. 159-167) | html | pdf | chapter contents |
    U. W. Arndt
    • 6.1.1. Overview  (p. 159) | html | pdf |
    • 6.1.2. Generation of X-rays  (pp. 159-162) | html | pdf |
    • 6.1.3. Properties of the X-ray beam  (pp. 162-164) | html | pdf |
    • 6.1.4. Beam conditioning  (pp. 164-166) | html | pdf |
    • References | html | pdf |
  • 6.2. Neutron sources  (pp. 168-176) | html | pdf | chapter contents |
    B. P. Schoenborn and R. Knott
    • 6.2.1. Reactors  (pp. 168-172) | html | pdf |
    • 6.2.2. Spallation neutron sources  (pp. 172-174) | html | pdf |
    • 6.2.3. Summary  (p. 175) | html | pdf |
    • References | html | pdf |

• X-ray detectors
  • 7.1. Comparison of X-ray detectors  (pp. 177-182) | html | pdf | chapter contents |
    S. M. Gruner, E. F. Eikenberry and M. W. Tate
    • 7.1.1. Commonly used detectors: general considerations  (pp. 177-178) | html | pdf |
    • 7.1.2. Evaluating and comparing detectors  (pp. 178-179) | html | pdf |
    • 7.1.3. Characteristics of different detector approaches  (pp. 179-181) | html | pdf |
    • 7.1.4. Future detectors  (p. 181) | html | pdf |
    • References | html | pdf |
  • 7.2. CCD detectors  (pp. 183-188) | html | pdf | chapter contents |
    M. W. Tate, E. F. Eikenberry and S. M. Gruner
    • 7.2.1. Overview  (p. 183) | html | pdf |
    • 7.2.2. CCD detector assembly  (pp. 183-184) | html | pdf |
    • 7.2.3. Calibration and correction  (pp. 184-186) | html | pdf |
    • 7.2.4. Detector system integration  (pp. 186-187) | html | pdf |
    • 7.2.5. Applications to macromolecular crystallography  (p. 187) | html | pdf |
    • 7.2.6. Future of CCD detectors  (p. 187) | html | pdf |
    • References | html | pdf |

• Synchrotron crystallography
  • 8.1. Synchrotron-radiation instrumentation, methods and scientific utilization  (pp. 189-204) | html | pdf | chapter contents |
    J. R. Helliwell
    • 8.1.1. Introduction  (p. 189) | html | pdf |
    • 8.1.2. The physics of SR  (pp. 189-190) | html | pdf |
    • 8.1.3. Insertion devices (IDs)  (pp. 190-191) | html | pdf |
    • 8.1.4. Beam characteristics delivered at the crystal sample  (pp. 191-192) | html | pdf |
    • 8.1.5. Evolution of SR machines and experiments  (pp. 192-194) | html | pdf |
    • 8.1.6. SR instrumentation  (pp. 194-195) | html | pdf |
    • 8.1.7. SR monochromatic and Laue diffraction geometry  (pp. 195-197) | html | pdf |
    • 8.1.8. Scientific utilization of SR in protein crystallography  (pp. 197-200) | html | pdf |
    • 8.1.9. Concluding remarks  (p. 200) | html | pdf |
    • References | html | pdf |
  • 8.2. Laue crystallography: time-resolved studies  (pp. 205-210) | html | pdf | chapter contents |
    K. Moffat
    • 8.2.1. Introduction  (p. 205) | html | pdf |
    • 8.2.2. Principles of Laue diffraction  (pp. 205-206) | html | pdf |
    • 8.2.3. Practical considerations in the Laue technique  (pp. 206-208) | html | pdf |
    • 8.2.4. The time-resolved experiment  (pp. 208-209) | html | pdf |
    • 8.2.5. Conclusions  (p. 209) | html | pdf |
    • References | html | pdf |

• X-ray data collection
  • 9.1. Principles of monochromatic data collection  (pp. 211-230) | html | pdf | chapter contents |
    Z. Dauter and K. S. Wilson
    • 9.1.1. Introduction  (p. 211) | html | pdf |
    • 9.1.2. The components of a monochromatic X-ray experiment  (p. 211) | html | pdf |
    • 9.1.3. Data completeness  (p. 211) | html | pdf |
    • 9.1.4. X-ray sources  (pp. 211-212) | html | pdf |
    • 9.1.5. Goniostat geometry  (pp. 212-213) | html | pdf |
    • 9.1.6. Basis of the rotation method  (pp. 213-217) | html | pdf |
    • 9.1.7. Rotation method: geometrical completeness  (pp. 217-221) | html | pdf |
    • 9.1.8. Crystal-to-detector distance  (pp. 221-222) | html | pdf |
    • 9.1.9. Wavelength  (p. 222) | html | pdf |
    • 9.1.10. Lysozyme as an example  (pp. 222-223) | html | pdf |
    • 9.1.11. Rotation method: qualitative factors  (pp. 223-225) | html | pdf |
    • 9.1.12. Radiation damage  (pp. 225-226) | html | pdf |
    • 9.1.13. Relating data collection to the problem in hand  (pp. 226-228) | html | pdf |
    • 9.1.14. The importance of low-resolution data  (p. 228) | html | pdf |
    • 9.1.15. Data quality over the whole resolution range  (pp. 228-229) | html | pdf |
    • 9.1.16. Strategies for automated data acquisition  (p. 229) | html | pdf |
    • 9.1.17. Final remarks  (p. 229) | html | pdf |
    • References | html | pdf |
  • 9.2. Robotic crystal loading  (pp. 231-233) | html | pdf | chapter contents |
    T. Earnest and C. Cork
    • 9.2.1. Introduction  (p. 231) | html | pdf |
    • 9.2.2. Robotic sample loaders  (pp. 231-233) | html | pdf |
    • 9.2.3. Conclusion  (p. 233) | html | pdf |
    • References | html | pdf |
  • 9.3. X-ray diffraction imaging of whole cells  (pp. 234-239) | html | pdf | chapter contents |
    D. Shapiro
    • 9.3.1. Introduction  (pp. 234-235) | html | pdf |
    • 9.3.2. Phase retrieval from single-particle diffraction data  (p. 235) | html | pdf |
    • 9.3.3. High-resolution imaging of yeast  (pp. 235-237) | html | pdf |
    • 9.3.4. Conclusions  (pp. 237-238) | html | pdf |
    • References | html | pdf |

• Cryocrystallography
  • 10.1. Introduction to cryocrystallography  (pp. 241-248) | html | pdf | chapter contents |
    H. Hope and S. Parkin
    • 10.1.1. Cooling of biocrystals  (pp. 241-242) | html | pdf |
    • 10.1.2. Beneficial effects of low temperature  (pp. 242-244) | html | pdf |
    • 10.1.3. Principles of cooling equipment  (pp. 244-245) | html | pdf |
    • 10.1.4. Operational considerations  (pp. 245-247) | html | pdf |
    • 10.1.5. Concluding note  (p. 247) | html | pdf |
    • References | html | pdf |
  • 10.2. Cryocrystallography techniques and devices  (pp. 249-255) | html | pdf | chapter contents |
    D. W. Rodgers
    • 10.2.1. Introduction  (p. 249) | html | pdf |
    • 10.2.2. Crystal preparation  (pp. 249-250) | html | pdf |
    • 10.2.3. Crystal mounting  (pp. 250-252) | html | pdf |
    • 10.2.4. Flash cooling  (pp. 252-253) | html | pdf |
    • 10.2.5. Transfer and storage  (pp. 253-254) | html | pdf |
    • References | html | pdf |
  • 10.3. Radiation damage  (pp. 256-261) | html | pdf | chapter contents |
    E. F. Garman
    • 10.3.1. Introduction  (p. 256) | html | pdf |
    • 10.3.2. Cryocrystallography as a mitigation strategy  (pp. 256-257) | html | pdf |
    • 10.3.3. Characteristics of radiation damage at cryotemperatures  (pp. 257-258) | html | pdf |
    • 10.3.4. Understanding radiation damage  (pp. 258-259) | html | pdf |
    • 10.3.5. Mitigating and correcting for radiation damage  (p. 259) | html | pdf |
    • 10.3.6. Using radiation damage  (p. 260) | html | pdf |
    • 10.3.7. Open questions  (p. 260) | html | pdf |
    • References | html | pdf |

• Data processing
  • 11.1. Automatic indexing of oscillation images  (pp. 263-265) | html | pdf | chapter contents |
    M. G. Rossmann
    • 11.1.1. Introduction  (p. 263) | html | pdf |
    • 11.1.2. The crystal orientation matrix  (p. 263) | html | pdf |
    • 11.1.3. Fourier analysis of the reciprocal-lattice vector distribution when projected onto a chosen direction  (pp. 263-264) | html | pdf |
    • 11.1.4. Exploring all possible directions to find a good set of basis vectors  (p. 264) | html | pdf |
    • 11.1.5. The program  (p. 265) | html | pdf |
    • References | html | pdf |
  • 11.2. Integration of macromolecular diffraction data  (pp. 266-271) | html | pdf | chapter contents |
    A. G. W. Leslie
    • 11.2.1. Introduction  (p. 266) | html | pdf |
    • 11.2.2. Prerequisites for accurate integration  (p. 266) | html | pdf |
    • 11.2.3. Methods of integration  (pp. 266-267) | html | pdf |
    • 11.2.4. The measurement box  (p. 267) | html | pdf |
    • 11.2.5. Integration by simple summation  (pp. 267-268) | html | pdf |
    • 11.2.6. Integration by profile fitting  (pp. 268-271) | html | pdf |
    • References | html | pdf |
  • 11.3. Integration, scaling, space-group assignment and post refinement  (pp. 272-281) | html | pdf | chapter contents |
    W. Kabsch
    • 11.3.1. Introduction  (p. 272) | html | pdf |
    • 11.3.2. Modelling rotation images  (pp. 272-275) | html | pdf |
    • 11.3.3. Integration  (pp. 275-277) | html | pdf |
    • 11.3.4. Scaling  (p. 277) | html | pdf |
    • 11.3.5. Post refinement  (pp. 277-278) | html | pdf |
    • 11.3.6. Space-group assignment  (pp. 278-280) | html | pdf |
    • References | html | pdf |
  • 11.4. DENZO and SCALEPACK  (pp. 282-295) | html | pdf | chapter contents |
    Z. Otwinowski, W. Minor, D. Borek and M. Cymborowski
    • 11.4.1. Introduction  (p. 282) | html | pdf |
    • 11.4.2. Diffraction from a perfect crystal lattice  (pp. 282-283) | html | pdf |
    • 11.4.3. Autoindexing  (pp. 283-284) | html | pdf |
    • 11.4.4. Coordinate systems  (pp. 284-285) | html | pdf |
    • 11.4.5. Experimental assumptions  (pp. 285-288) | html | pdf |
    • 11.4.6. Prediction of the diffraction pattern  (pp. 288-289) | html | pdf |
    • 11.4.7. Integration of diffraction maxima by profile fitting  (p. 289) | html | pdf |
    • 11.4.8. Scaling – multiplicative corrections  (pp. 289-291) | html | pdf |
    • 11.4.9. Global refinement or post refinement  (p. 291) | html | pdf |
    • 11.4.10. Merging – assessment of the error model and signal magnitudes in the data  (pp. 291-292) | html | pdf |
    • 11.4.11. Detector diagnostics  (p. 292) | html | pdf |
    • 11.4.12. HKL-2000 and HKL-3000  (pp. 292-294) | html | pdf |
    • 11.4.13. Final note  (p. 294) | html | pdf |
    • References | html | pdf |
  • 11.5. The use of partially recorded reflections for post refinement, scaling and averaging X-ray diffraction data  (pp. 296-303) | html | pdf | chapter contents |
    C. G. van Beek, R. Bolotovsky and M. G. Rossmann
    • 11.5.1. Introduction  (p. 296) | html | pdf |
    • 11.5.2. Generalization of the Hamilton, Rollett and Sparks equations to take into account partial reflections  (pp. 296-297) | html | pdf |
    • 11.5.3. Selection of reflections useful for scaling  (p. 297) | html | pdf |
    • 11.5.4. Restraints and constraints  (pp. 297-298) | html | pdf |
    • 11.5.5. Generalization of the procedure for averaging reflection intensities  (p. 298) | html | pdf |
    • 11.5.6. Estimating the quality of data scaling and averaging  (p. 298) | html | pdf |
    • 11.5.7. Experimental results  (pp. 298-301) | html | pdf |
    • 11.5.8. Conclusions  (p. 301) | html | pdf |
    • Appendix 11.5.1. Partiality model (Rossmann, 1979; Rossmann et al., 1979)  (pp. 301-302) | html | pdf |
    • References | html | pdf |
  • 11.6. XDS  (pp. 304-310) | html | pdf | chapter contents |
    W. Kabsch
    • 11.6.1. Functional specification  (p. 304) | html | pdf |
    • 11.6.2. XDS  (pp. 304-308) | html | pdf |
    • 11.6.3. XSCALE  (pp. 308-309) | html | pdf |
    • 11.6.4. XDSCONV  (p. 309) | html | pdf |
    • 11.6.5. Parallelization of XDS  (pp. 309-310) | html | pdf |
    • 11.6.6. Availability  (p. 310) | html | pdf |
    • References | html | pdf |
  • 11.7. Detecting twinning by merohedry  (pp. 311-316) | html | pdf | chapter contents |
    T. O. Yeates and Y. Tsai
    • 11.7.1. Introduction  (p. 311) | html | pdf |
    • 11.7.2. Twinning by merohedry – considerations of lattice symmetry  (pp. 311-312) | html | pdf |
    • 11.7.3. Considerations of length scale and effects in reciprocal space  (p. 312) | html | pdf |
    • 11.7.4. Extent of twinning: the twin fraction  (p. 312) | html | pdf |
    • 11.7.5. Indications of twinning  (pp. 312-313) | html | pdf |
    • 11.7.6. Twinning tests based on overall intensity statistics  (pp. 313-314) | html | pdf |
    • 11.7.7. Tests for partial twinning based on comparison of twin-related reflections  (pp. 314-315) | html | pdf |
    • 11.7.8. Higher forms of twinning  (p. 315) | html | pdf |
    • 11.7.9. Other kinds of disorder  (p. 315) | html | pdf |
    • 11.7.10. Summary  (p. 315) | 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. 317-326) | html | pdf | chapter contents |
    D. Carvin, S. A. Islam, M. J. E. Sternberg and T. L. Blundell
    • 12.1.1. Introduction  (p. 317) | html | pdf |
    • 12.1.2. Heavy-atom data bank  (pp. 317-318) | html | pdf |
    • 12.1.3. Properties of heavy-atom compounds and their complexes  (pp. 318-320) | html | pdf |
    • 12.1.4. Amino acids as ligands  (pp. 320-321) | html | pdf |
    • 12.1.5. Protein chemistry of heavy-atom reagents  (pp. 321-324) | html | pdf |
    • 12.1.6. Metal-ion replacement in metalloproteins  (p. 324) | html | pdf |
    • 12.1.7. Analogues of amino acids  (pp. 324-325) | html | pdf |
    • 12.1.8. Use of the heavy-atom data bank to select derivatives  (p. 325) | html | pdf |
    • References | html | pdf |
  • 12.2. Locating heavy-atom sites  (pp. 327-332) | html | pdf | chapter contents |
    M. T. Stubbs and R. Huber
    • 12.2.1. The origin of the phase problem  (pp. 327-328) | html | pdf |
    • 12.2.2. The Patterson function  (pp. 328-329) | html | pdf |
    • 12.2.3. The difference Fourier  (p. 329) | html | pdf |
    • 12.2.4. Reality  (pp. 329-330) | html | pdf |
    • 12.2.5. Special complications   (pp. 330-331) | html | pdf |
    • References | html | pdf |

• Molecular replacement
  • 13.1. Noncrystallographic symmetry  (pp. 333-339) | html | pdf | chapter contents |
    D. M. Blow
    • 13.1.1. Introduction  (p. 333) | html | pdf |
    • 13.1.2. Definition of noncrystallographic symmetry  (p. 333) | html | pdf |
    • 13.1.3. Use of the Patterson function to interpret noncrystallographic symmetry  (pp. 333-335) | html | pdf |
    • 13.1.4. Interpretation of generalized noncrystallographic symmetry where the molecular structure is partially known  (p. 335) | html | pdf |
    • 13.1.5. The power of noncrystallographic symmetry in structure analysis  (pp. 336-338) | html | pdf |
    • References | html | pdf |
  • 13.2. Rotation functions  (pp. 340-346) | html | pdf | chapter contents |
    J. Navaza
    • 13.2.1. Overview  (p. 340) | html | pdf |
    • 13.2.2. Rotations in three-dimensional Euclidean space  (pp. 340-341) | html | pdf |
    • 13.2.3. The rotation function  (pp. 341-343) | html | pdf |
    • 13.2.4. The locked rotation function  (pp. 343-344) | html | pdf |
    • 13.2.5. Other rotation functions  (p. 344) | html | pdf |
    • 13.2.6. Concluding remarks  (p. 344) | html | pdf |
    • Appendix 13.2.1. Formulae for the derivation and computation of the fast rotation function  (pp. 344-346) | html | pdf |
    • References | html | pdf |
  • 13.3. Translation functions  (pp. 347-351) | html | pdf | chapter contents |
    L. Tong
    • 13.3.1. Introduction  (p. 347) | html | pdf |
    • 13.3.2. R-factor and correlation-coefficient translation functions  (pp. 347-348) | html | pdf |
    • 13.3.3. Patterson-correlation translation function  (p. 348) | html | pdf |
    • 13.3.4. Phased translation function  (p. 349) | html | pdf |
    • 13.3.5. Packing check in translation functions  (p. 349) | html | pdf |
    • 13.3.6. The unique region of a translation function (the Cheshire group)  (p. 349) | html | pdf |
    • 13.3.7. Combined molecular replacement  (pp. 349-350) | html | pdf |
    • 13.3.8. The locked translation function  (p. 350) | html | pdf |
    • 13.3.9. Miscellaneous translation functions  (p. 350) | html | pdf |
    • References | html | pdf |
  • 13.4. Noncrystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension  (pp. 352-363) | html | pdf | chapter contents |
    M. G. Rossmann and E. Arnold
    • 13.4.1. Introduction  (p. 352) | html | pdf |
    • 13.4.2. Noncrystallographic symmetry (NCS)  (pp. 352-354) | html | pdf |
    • 13.4.3. Phase determination using NCS  (p. 354) | html | pdf |
    • 13.4.4. The p- and h-cells  (pp. 354-355) | html | pdf |
    • 13.4.5. Combining crystallographic and noncrystallographic symmetry  (pp. 355-356) | html | pdf |
    • 13.4.6. Determining the molecular envelope  (pp. 356-357) | html | pdf |
    • 13.4.7. Finding the averaged density  (pp. 357-358) | html | pdf |
    • 13.4.8. Interpolation  (p. 358) | html | pdf |
    • 13.4.9. Combining different crystal forms  (p. 358) | html | pdf |
    • 13.4.10. Phase extension and refinement of the NCS parameters  (p. 359) | html | pdf |
    • 13.4.11. Convergence  (pp. 359-360) | html | pdf |
    • 13.4.12. Ab initio phasing starts  (p. 360) | html | pdf |
    • 13.4.13. Recent salient examples in low-symmetry cases: multidomain averaging and systematic applications of multiple-crystal-form averaging  (pp. 360-361) | html | pdf |
    • 13.4.14. Programs  (p. 361) | html | pdf |
    • References | html | pdf |
  • 13.5. Molecular replacement with MOLREP  (pp. 364-366) | html | pdf | chapter contents |
    A. Vagin and A. Teplyakov
    • 13.5.1. Introduction  (p. 364) | html | pdf |
    • 13.5.2. Program operation  (p. 364) | html | pdf |
    • 13.5.3. Preparation of the search model  (p. 364) | html | pdf |
    • 13.5.4. Preparation of the X-ray data  (pp. 364-365) | html | pdf |
    • 13.5.5. Rotational search  (p. 365) | html | pdf |
    • 13.5.6. Positional search  (p. 365) | html | pdf |
    • 13.5.7. Multi-copy search  (pp. 365-366) | html | pdf |
    • 13.5.8. Fitting the model into electron density  (p. 366) | html | pdf |
    • 13.5.9. Distribution  (p. 366) | html | pdf |
    • References | html | pdf |

• Anomalous dispersion
  • 14.1. Heavy-atom location and phase determination with single-wavelength diffraction data  (pp. 367-372) | html | pdf | chapter contents |
    B. W. Matthews
    • 14.1.1. Introduction  (p. 367) | html | pdf |
    • 14.1.2. The isomorphous-replacement method  (pp. 367-368) | html | pdf |
    • 14.1.3. The method of multiple isomorphous replacement  (p. 368) | html | pdf |
    • 14.1.4. The method of Blow & Crick  (pp. 368-369) | html | pdf |
    • 14.1.5. The best Fourier  (p. 369) | html | pdf |
    • 14.1.6. Anomalous scattering  (p. 369) | html | pdf |
    • 14.1.7. Theory of anomalous scattering  (pp. 369-370) | html | pdf |
    • 14.1.8. The phase probability distribution for anomalous scattering  (pp. 370-371) | html | pdf |
    • 14.1.9. Anomalous scattering without isomorphous replacement  (p. 371) | html | pdf |
    • 14.1.10. Location of heavy-atom sites  (p. 371) | html | pdf |
    • 14.1.11. Use of anomalous-scattering data in heavy-atom location  (p. 371) | html | pdf |
    • 14.1.12. Use of difference Fourier syntheses  (p. 371) | html | pdf |
    • 14.1.13. Single isomorphous replacement  (pp. 371-372) | html | pdf |
    • References | html | pdf |
  • 14.2. Multiwavelength anomalous diffraction  (pp. 373-378) | html | pdf | chapter contents |
    J. L. Smith and W. A. Hendrickson
    • 14.2.1. Anomalous scattering factors  (pp. 373-374) | html | pdf |
    • 14.2.2. A phase equation for MAD  (pp. 374-375) | html | pdf |
    • 14.2.3. Diffraction ratios for estimating the MAD phasing signal  (p. 375) | html | pdf |
    • 14.2.4. Experimental considerations  (pp. 375-376) | html | pdf |
    • 14.2.5. Data handling  (p. 376) | html | pdf |
    • 14.2.6. Approaches to MAD phasing  (pp. 376-377) | html | pdf |
    • 14.2.7. Determination of the anomalous-scatterer partial structure  (p. 377) | html | pdf |
    • 14.2.8. General anomalous-scatterer labels for biological macromolecules  (pp. 377-378) | html | pdf |
    • References | html | pdf |
  • 14.3. Automated MAD and MIR structure solution  (pp. 379-383) | html | pdf | chapter contents |
    T. C. Terwilliger and J. Berendzen
    • 14.3.1. Introduction  (p. 379) | html | pdf |
    • 14.3.2. MAD and MIR structure solution  (p. 379) | html | pdf |
    • 14.3.3. Decision making and structure solution  (p. 379) | html | pdf |
    • 14.3.4. The need for rapid refinement and phasing during automated structure solution  (p. 379) | html | pdf |
    • 14.3.5. Conversion of MAD data to a pseudo-SIRAS form  (pp. 379-380) | html | pdf |
    • 14.3.6. Scoring of trial heavy-atom solutions  (pp. 380-381) | html | pdf |
    • 14.3.7. Automated MIR and MAD structure determination  (pp. 381-382) | html | pdf |
    • 14.3.8. Generation of model X-ray data sets  (p. 382) | html | pdf |
    • 14.3.9. Conclusions  (p. 382) | html | pdf |
    • 14.3.10. Software availability  (p. 382) | html | pdf |
    • References | html | pdf |

• Density modification and phase combination
  • 15.1. Phase improvement by iterative density modification  (pp. 385-400) | html | pdf | chapter contents |
    K. Y. J. Zhang, K. D. Cowtan and P. Main
    • 15.1.1. Introduction  (p. 385) | html | pdf |
    • 15.1.2. Density-modification methods  (pp. 385-393) | html | pdf |
    • 15.1.3. Reciprocal-space interpretation of density modification  (pp. 393-394) | html | pdf |
    • 15.1.4. Phase combination  (pp. 394-396) | html | pdf |
    • 15.1.5. Combining constraints for phase improvement  (pp. 396-398) | html | pdf |
    • 15.1.6. Statistical density-modification methods  (p. 398) | html | pdf |
    • 15.1.7. Example  (pp. 398-399) | html | pdf |
    • References | html | pdf |
  • 15.2. Model phases: probabilities, bias and maps  (pp. 401-406) | html | pdf | chapter contents |
    R. J. Read
    • 15.2.1. Introduction  (p. 401) | html | pdf |
    • 15.2.2. Model bias: importance of phase  (p. 401) | html | pdf |
    • 15.2.3. Structure-factor probability relationships  (pp. 401-403) | html | pdf |
    • 15.2.4. Figure-of-merit weighting for model phases  (p. 404) | html | pdf |
    • 15.2.5. Map coefficients to reduce model bias  (p. 404) | html | pdf |
    • 15.2.6. Estimation of overall coordinate error  (pp. 404-405) | html | pdf |
    • 15.2.7. Difference-map coefficients  (p. 405) | html | pdf |
    • 15.2.8. Refinement bias  (p. 405) | html | pdf |
    • References | html | pdf |
  • 15.3. DM/DMMULTI software for phase improvement by density modification  (pp. 407-412) | html | pdf | chapter contents |
    K. D. Cowtan, K. Y. J. Zhang and P. Main
    • 15.3.1. Introduction  (p. 407) | html | pdf |
    • 15.3.2. Program operation  (p. 407) | html | pdf |
    • 15.3.3. Preparation of input data  (pp. 407-408) | html | pdf |
    • 15.3.4. Choice of modes  (pp. 408-410) | html | pdf |
    • 15.3.5. Code description  (pp. 410-412) | html | pdf |
    • References | html | pdf |

• Direct methods
  • 16.1. Ab initio phasing  (pp. 413-432) | html | pdf | chapter contents |
    G. M. Sheldrick, C. J. Gilmore, H. A. Hauptman, C. M. Weeks, R. Miller and I. Usón
    • 16.1.1. Introduction  (pp. 413-415) | html | pdf |
    • 16.1.2. Normalized structure-factor magnitudes  (pp. 415-416) | html | pdf |
    • 16.1.3. Starting the phasing process  (pp. 416-417) | html | pdf |
    • 16.1.4. Reciprocal-space phase refinement or expansion (shaking)  (pp. 417-418) | html | pdf |
    • 16.1.5. Real-space constraints (baking)  (pp. 418-419) | html | pdf |
    • 16.1.6. Fourier refinement  (p. 419) | html | pdf |
    • 16.1.7. Resolution enhancement: the `free lunch' algorithm  (p. 419) | html | pdf |
    • 16.1.8. Utilizing Pattersons for better starts  (pp. 419-420) | html | pdf |
    • 16.1.9. Shake-and-Bake: an analysis of a dual-space method in action  (pp. 420-422) | html | pdf |
    • 16.1.10. Applying dual-space programs successfully  (pp. 422-425) | html | pdf |
    • 16.1.11. Substructure solution for native sulfurs and halide soaks  (pp. 425-426) | html | pdf |
    • 16.1.12. Computer programs for dual-space phasing  (pp. 426-429) | html | pdf |
    • 16.1.13. Conclusions and the grand challenge  (p. 429) | html | pdf |
    • References | html | pdf |
  • 16.2. The maximum-entropy method  (pp. 433-436) | html | pdf | chapter contents |
    G. Bricogne
    • 16.2.1. Introduction  (p. 433) | html | pdf |
    • 16.2.2. The maximum-entropy principle in a general context  (pp. 433-435) | html | pdf |
    • 16.2.3. Adaptation to crystallography  (pp. 435-436) | html | pdf |
    • References | html | pdf |
  • 16.3. Ab initio phasing of low-resolution Fourier syntheses  (pp. 437-442) | html | pdf | chapter contents |
    V. Y. Lunin, A. G. Urzhumtsev and A. Podjarny
    • 16.3.1. Introduction  (p. 437) | html | pdf |
    • 16.3.2. General features of low-resolution images  (p. 437) | html | pdf |
    • 16.3.3. Low-resolution phasing  (pp. 437-438) | html | pdf |
    • 16.3.4. Phase generation and selection  (pp. 438-439) | html | pdf |
    • 16.3.5. Processing of the output  (pp. 439-441) | html | pdf |
    • 16.3.6. Conclusions and examples  (p. 441) | html | pdf |
    • References | html | pdf |

• Model building and computer graphics
  • 17.1. Macromolecular model building and validation using Coot  (pp. 443-447) | html | pdf | chapter contents |
    P. Emsley, B. Lohkamp and K. Cowtan
    • 17.1.1. Introduction  (p. 443) | html | pdf |
    • 17.1.2. Model building  (pp. 443-445) | html | pdf |
    • 17.1.3. Validation  (pp. 445-446) | html | pdf |
    • 17.1.4. Scripting  (p. 446) | html | pdf |
    • 17.1.5. Discussion  (p. 446) | html | pdf |
    • References | html | pdf |
  • 17.2. Molecular graphics and animation  (pp. 448-458) | html | pdf | chapter contents |
    A. J. Olson
    • 17.2.1. Introduction  (p. 448) | html | pdf |
    • 17.2.2. Background – the evolution of molecular graphics hardware and software   (pp. 448-449) | html | pdf |
    • 17.2.3. Representation and visualization of molecular data and models  (pp. 449-454) | html | pdf |
    • 17.2.4. Presentation graphics  (pp. 454-457) | html | pdf |
    • 17.2.5. Looking ahead  (p. 457) | html | pdf |
    • References | html | pdf |

• Refinement
  • 18.1. Introduction to refinement  (pp. 459-465) | html | pdf | chapter contents |
    L. F. Ten Eyck and K. D. Watenpaugh
    • 18.1.1. Overview  (p. 459) | html | pdf |
    • 18.1.2. Background  (p. 459) | html | pdf |
    • 18.1.3. Objectives  (p. 459) | html | pdf |
    • 18.1.4. Least squares and maximum likelihood  (p. 460) | html | pdf |
    • 18.1.5. Optimization  (p. 460) | html | pdf |
    • 18.1.6. Data  (p. 460) | html | pdf |
    • 18.1.7. Models  (pp. 461-462) | html | pdf |
    • 18.1.8. Optimization methods  (pp. 462-463) | html | pdf |
    • 18.1.9. Evaluation of the model  (p. 464) | html | pdf |
    • 18.1.10. Conclusion  (p. 464) | html | pdf |
    • References | html | pdf |
  • 18.2. Enhanced macromolecular refinement by simulated annealing  (pp. 466-473) | html | pdf | chapter contents |
    A. T. Brunger, P. D. Adams and L. M. Rice
    • 18.2.1. Introduction  (p. 466) | html | pdf |
    • 18.2.2. Cross validation  (pp. 466-467) | html | pdf |
    • 18.2.3. The target function  (pp. 467-468) | html | pdf |
    • 18.2.4. Searching conformational space  (pp. 468-470) | html | pdf |
    • 18.2.5. Examples  (pp. 470-471) | html | pdf |
    • 18.2.6. Multi-start refinement and structure-factor averaging  (p. 471) | html | pdf |
    • 18.2.7. Ensemble models  (pp. 471-472) | html | pdf |
    • 18.2.8. Conclusions  (p. 472) | html | pdf |
    • References | html | pdf |
  • 18.3. Structure quality and target parameters  (pp. 474-484) | html | pdf | chapter contents |
    R. A. Engh and R. Huber
    • 18.3.1. Purpose of restraints  (p. 474) | html | pdf |
    • 18.3.2. Formulation of refinement restraints  (pp. 475-483) | html | pdf |
    • 18.3.3. Strategy of application during building/refinement  (p. 483) | html | pdf |
    • 18.3.4. Future perspectives  (p. 483) | html | pdf |
    • References | html | pdf |
  • 18.4. Refinement at atomic resolution  (pp. 485-498) | html | pdf | chapter contents |
    Z. Dauter, G. N. Murshudov and K. S. Wilson
    • 18.4.1. The atomic model and a definition of atomic resolution  (pp. 485-487) | html | pdf |
    • 18.4.2. Data  (pp. 487-488) | html | pdf |
    • 18.4.3. Computational algorithms and strategies  (pp. 488-489) | html | pdf |
    • 18.4.4. Computational options and tactics  (pp. 489-491) | html | pdf |
    • 18.4.5. Features in the refined model  (pp. 491-495) | html | pdf |
    • 18.4.6. Quality assessment of the model  (p. 495) | html | pdf |
    • 18.4.7. Relation to biological chemistry   (pp. 495-496) | html | pdf |
    • 18.4.8. Practical strategies  (p. 496) | html | pdf |
    • References | html | pdf |
  • 18.5. Coordinate uncertainty  (pp. 499-511) | html | pdf | chapter contents |
    D. W. J. Cruickshank
    • 18.5.1. Introduction  (pp. 499-500) | html | pdf |
    • 18.5.2. The least-squares method  (pp. 500-501) | html | pdf |
    • 18.5.3. Restrained refinement  (pp. 501-502) | html | pdf |
    • 18.5.4. Two examples of full-matrix inversion  (pp. 502-505) | html | pdf |
    • 18.5.5. Approximate methods  (pp. 505-506) | html | pdf |
    • 18.5.6. The diffraction-component precision index  (pp. 506-507) | html | pdf |
    • 18.5.7. Examples of the diffraction-component precision index  (pp. 507-509) | html | pdf |
    • 18.5.8. Luzzati plots  (pp. 509-510) | html | pdf |
    • References | html | pdf |
  • 18.6. CNS, a program system for structure-determination and refinement  (pp. 512-519) | html | pdf | chapter contents |
    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
    • 18.6.1. Introduction  (p. 512) | html | pdf |
    • 18.6.2. The CNS language  (pp. 512-513) | html | pdf |
    • 18.6.3. Symbols and parameters  (p. 513) | html | pdf |
    • 18.6.4. Statistical functions  (pp. 513-514) | html | pdf |
    • 18.6.5. Symbolic target function  (pp. 514-515) | html | pdf |
    • 18.6.6. Modules and procedures  (pp. 515-516) | html | pdf |
    • 18.6.7. Task files  (p. 516) | html | pdf |
    • 18.6.8. HTML interface  (pp. 516-517) | html | pdf |
    • 18.6.9. Example: combined maximum-likelihood and simulated-annealing refinement  (p. 517) | html | pdf |
    • 18.6.10. Conclusions  (p. 517) | html | pdf |
    • References | html | pdf |
  • 18.7. The TNT refinement package  (pp. 520-524) | html | pdf | chapter contents |
    D. E. Tronrud and L. F. Ten Eyck
    • 18.7.1. Scope and function of the package  (p. 520) | html | pdf |
    • 18.7.2. Historical context  (p. 520) | html | pdf |
    • 18.7.3. Design principles  (pp. 520-522) | html | pdf |
    • 18.7.4. Current structure of the package  (p. 522) | html | pdf |
    • 18.7.5. Innovations first introduced in TNT  (pp. 522-523) | html | pdf |
    • 18.7.6. TNT as a research tool  (p. 523) | html | pdf |
    • 18.7.7. Current status of TNT  (p. 523) | html | pdf |
    • References | html | pdf |
  • 18.8. ARP/wARP – automated model building and refinement  (pp. 525-528) | html | pdf | chapter contents |
    V. S. Lamzin, A. Perrakis and K. S. Wilson
    • 18.8.1. Refinement and model building are two parts of modelling a structure  (p. 525) | html | pdf |
    • 18.8.2. Free-atom and hybrid models  (pp. 525-526) | html | pdf |
    • 18.8.3. ARP/wARP applications  (pp. 526-528) | html | pdf |
    • 18.8.4. Iterations  (p. 528) | html | pdf |
    • 18.8.5. Applicability and requirements  (p. 528) | html | pdf |
    • References | html | pdf |
  • 18.9. Macromolecular applications of SHELX  (pp. 529-533) | html | pdf | chapter contents |
    G. M. Sheldrick
    • 18.9.1. Introduction  (p. 529) | html | pdf |
    • 18.9.2. Experimental phasing with SHELXC/D/E  (pp. 529-530) | html | pdf |
    • 18.9.3. Macromolecular refinement using SHELXL  (pp. 531-532) | html | pdf |
    • 18.9.4. SHELXPRO – protein interface to SHELX  (p. 532) | html | pdf |
    • 18.9.5. Distribution and support of SHELX  (p. 532) | html | pdf |
    • References | html | pdf |
  • 18.10. PrimeX and the Schrödinger computational chemistry suite of programs   (pp. 534-538) | html | pdf | chapter contents |
    J. A. Bell, Y. Cao, J. R. Gunn, T. Day, E. Gallicchio, Z. Zhou, R. Levy and R. Farid
    • 18.10.1. Introduction  (p. 534) | html | pdf |
    • 18.10.2. Computational environment  (pp. 534-535) | html | pdf |
    • 18.10.3. Achieving the mission of PrimeX  (pp. 535-536) | html | pdf |
    • 18.10.4. PrimeX implementation and theory  (pp. 536-538) | html | pdf |
    • 18.10.5. Conclusion  (p. 538) | html | pdf |
    • References | html | pdf |
  • 18.11. PHENIX: a comprehensive Python-based system for macromolecular structure solution  (pp. 539-547) | html | pdf | chapter contents |
    P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart
    • 18.11.1. Foundations  (p. 539) | html | pdf |
    • 18.11.2. Analysis of experimental data  (p. 540) | html | pdf |
    • 18.11.3. Substructure determination, phasing and molecular replacement  (pp. 540-541) | html | pdf |
    • 18.11.4. Model building, ligand fitting and nucleic acids  (pp. 541-542) | html | pdf |
    • 18.11.5. Model, and model-to-data, validation  (pp. 542-543) | html | pdf |
    • 18.11.6. Structure refinement  (pp. 543-544) | html | pdf |
    • 18.11.7. Integrated structure determination  (pp. 544-545) | html | pdf |
    • 18.11.8. Conclusions  (p. 545) | html | pdf |
    • References | html | pdf |
  • 18.12. Structure determination in the presence of twinning by merohedry  (pp. 548-551) | html | pdf | chapter contents |
    T. O. Yeates and M. R. Sawaya
    • 18.12.1. Introduction  (p. 548) | html | pdf |
    • 18.12.2. Detwinning based on observed intensities  (p. 548) | html | pdf |
    • 18.12.3. Molecular replacement with twinning  (p. 548) | html | pdf |
    • 18.12.4. Multiple isomorphous replacement and anomalous phasing with twinning  (pp. 548-549) | html | pdf |
    • 18.12.5. Atomic refinement with twinning  (pp. 549-550) | html | pdf |
    • 18.12.6. Detwinning on the basis of model F_calc values  (p. 550) | html | pdf |
    • 18.12.7. Summary  (pp. 550-551) | html | pdf |
    • References | html | pdf |

• Other experimental techniques
  • 19.1. Neutron crystallography: methods and information content  (pp. 553-556) | html | pdf | chapter contents |
    A. A. Kossiakoff
    • 19.1.1. Introduction  (p. 553) | html | pdf |
    • 19.1.2. Diffraction geometries  (p. 553) | html | pdf |
    • 19.1.3. Neutron density maps – information content  (pp. 553-554) | html | pdf |
    • 19.1.4. Phasing models and evaluation of correctness  (p. 554) | html | pdf |
    • 19.1.5. Evaluation of correctness  (pp. 554-555) | html | pdf |
    • 19.1.6. Refinement  (p. 555) | html | pdf |
    • 19.1.7. D₂O − H₂O solvent difference maps  (p. 555) | html | pdf |
    • 19.1.8. Applications of D₂O − H₂O solvent difference maps  (pp. 555-556) | html | pdf |
    • References | html | pdf |
  • 19.2. Electron diffraction of protein crystals  (pp. 557-562) | html | pdf | chapter contents |
    W. Chiu
    • 19.2.1. Electron scattering  (p. 557) | html | pdf |
    • 19.2.2. The electron microscope  (p. 557) | html | pdf |
    • 19.2.3. Data collection  (pp. 557-558) | html | pdf |
    • 19.2.4. Data processing  (pp. 558-561) | html | pdf |
    • 19.2.5. Future development  (p. 561) | html | pdf |
    • References | html | pdf |
  • 19.3. Small-angle X-ray scattering  (pp. 563-574) | html | pdf | chapter contents |
    H. Tsuruta and J. E. Johnson
    • 19.3.1. Introduction  (p. 563) | html | pdf |
    • 19.3.2. Small-angle single-crystal X-ray diffraction studies  (pp. 563-564) | html | pdf |
    • 19.3.3. Solution X-ray scattering studies  (pp. 564-573) | html | pdf |
  • 19.4. Small-angle neutron scattering  (pp. 575-582) | html | pdf | chapter contents |
    D. M. Engelman and P. B. Moore
    • 19.4.1. Introduction  (p. 575) | html | pdf |
    • 19.4.2. Fundamental relationships  (pp. 575-577) | html | pdf |
    • 19.4.3. Contrast variation  (pp. 577-579) | html | pdf |
    • 19.4.4. Distance measurements  (pp. 579-580) | html | pdf |
    • 19.4.5. Practical considerations  (p. 580) | html | pdf |
    • 19.4.6. Examples  (pp. 580-581) | html | pdf |
    • References | html | pdf |
  • 19.5. Fibre diffraction  (pp. 583-592) | html | pdf | chapter contents |
    R. Chandrasekaran and G. Stubbs
    • 19.5.1. Introduction  (p. 583) | html | pdf |
    • 19.5.2. Types of fibres  (pp. 583-584) | html | pdf |
    • 19.5.3. Diffraction by helical molecules  (pp. 584-585) | html | pdf |
    • 19.5.4. Fibre preparation  (p. 585) | html | pdf |
    • 19.5.5. Data collection  (p. 585) | html | pdf |
    • 19.5.6. Data processing  (pp. 585-586) | html | pdf |
    • 19.5.7. Determination of structures  (pp. 586-588) | html | pdf |
    • 19.5.8. Structures determined by X-ray fibre diffraction  (pp. 588-590) | html | pdf |
    • References | html | pdf |
  • 19.6. Electron cryomicroscopy of biological macromolecules  (pp. 593-614) | html | pdf | chapter contents |
    T. S. Baker and R. Henderson
    • 19.6.1. Abbreviations used  (p. 593) | html | pdf |
    • 19.6.2. Introduction: macromolecular structure determination using electron microscopy  (p. 593) | html | pdf |
    • 19.6.3. Physics of electron scattering and radiation damage  (pp. 593-595) | html | pdf |
    • 19.6.4. Three-dimensional electron cryomicroscopy of macromolecules  (pp. 595-601) | html | pdf |
    • 19.6.5. Image processing and 3D reconstruction  (pp. 601-604) | html | pdf |
    • 19.6.6. Visualization, modelling and interpretation of results  (pp. 604-605) | html | pdf |
    • 19.6.7. Trends  (pp. 605-606) | html | pdf |
    • References | html | pdf |
  • 19.7. Nuclear magnetic resonance (NMR) spectroscopy  (pp. 615-619) | html | pdf | chapter contents |
    K. Wüthrich
    • 19.7.1. Complementary roles of NMR in solution and X-ray crystallography in structural biology  (p. 615) | html | pdf |
    • 19.7.2. A standard protocol for NMR structure determination of proteins and nucleic acids  (pp. 615-617) | html | pdf |
    • 19.7.3. Combined use of single-crystal X-ray diffraction and solution NMR for structure determination  (p. 617) | html | pdf |
    • 19.7.4. NMR studies of solvation in solution  (pp. 617-618) | html | pdf |
    • 19.7.5. NMR studies of rate processes and conformational equilibria in three-dimensional macromolecular structures  (p. 618) | html | pdf |
    • References | html | pdf |
  • 19.8. Use of SPIDER and SPIRE in image reconstruction  (pp. 620-623) | html | pdf | chapter contents |
    A. Leith, W. Baxter and J. Frank
    • 19.8.1. Introduction  (p. 620) | html | pdf |
    • 19.8.2. Basic philosophy of single-particle reconstruction  (pp. 620-621) | html | pdf |
    • 19.8.3. Implementation of single-particle reconstruction in SPIDER  (pp. 621-623) | html | pdf |
    • 19.8.4. Implementation of single-particle reconstruction in SPIRE  (p. 623) | html | pdf |
    • 19.8.5. Conclusion  (p. 623) | html | pdf |
    • References | html | pdf |
  • 19.9. Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D  (pp. 624-628) | html | pdf | chapter contents |
    M. van Heel, R. Portugal, A. Rohou, C. Linnemayr, C. Bebeacua, R. Schmidt, T. Grant and M. Schatz
    • 19.9.1. Introduction  (p. 624) | html | pdf |
    • 19.9.2. The IMAGIC software system  (p. 624) | html | pdf |
    • 19.9.3. IMAGIC `4D' processing/data format  (pp. 624-625) | html | pdf |
    • 19.9.4. Software parallelization  (p. 625) | html | pdf |
    • 19.9.5. Full 2D (parallel) astigmatic contrast transfer function correction  (p. 625) | html | pdf |
    • 19.9.6. Parallel automatic particle picking  (p. 625) | html | pdf |
    • 19.9.7. Parallel multi-reference alignments and reference bias  (p. 626) | html | pdf |
    • 19.9.8. MSA and its parallelization  (p. 626) | html | pdf |
    • 19.9.9. Handling multiple 3D reconstructions in parallel  (pp. 626-627) | html | pdf |
    • 19.9.10. Angular reconstitution 4D refinements  (p. 627) | html | pdf |
    • 19.9.11. Discussion  (p. 627) | html | pdf |
    • References | html | pdf |
  • 19.10. Single-particle reconstruction with EMAN  (pp. 629-632) | html | pdf | chapter contents |
    S. Ludtke
    • 19.10.1. Introduction  (p. 629) | html | pdf |
    • 19.10.2. Overview of EMAN  (pp. 629-630) | html | pdf |
    • 19.10.3. Single-particle reconstruction  (p. 631) | html | pdf |
    • 19.10.4. Evaluating the reconstruction  (pp. 631-632) | 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. 633-641) | html | pdf | chapter contents |
    U. Stocker and W. F. van Gunsteren
    • 20.1.1. Introduction  (p. 633) | html | pdf |
    • 20.1.2. Methods  (pp. 633-634) | html | pdf |
    • 20.1.3. Results  (pp. 634-640) | html | pdf |
    • 20.1.4. Conclusions  (p. 640) | html | pdf |
    • References | html | pdf |
  • 20.2. Molecular-dynamics simulations of biological macromolecules  (pp. 642-648) | html | pdf | chapter contents |
    C. B. Post and V. M. Dadarlat
    • 20.2.1. Introduction  (p. 642) | html | pdf |
    • 20.2.2. The simulation method  (p. 642) | html | pdf |
    • 20.2.3. Potential-energy function  (pp. 642-644) | html | pdf |
    • 20.2.4. Empirical parameterization of the force field  (p. 644) | html | pdf |
    • 20.2.5. Modifications in the force field for structure determination  (p. 644) | html | pdf |
    • 20.2.6. Internal dynamics and average structures  (pp. 644-645) | html | pdf |
    • 20.2.7. Assessment of the simulation procedure  (p. 645) | html | pdf |
    • 20.2.8. Effect of crystallographic atomic resolution on structural stability during molecular dynamics  (pp. 645-647) | html | pdf |
    • References | html | pdf |

• Structure validation
  • 21.1. Validation of protein crystal structures  (pp. 649-661) | html | pdf | chapter contents |
    G. J. Kleywegt
    • 21.1.1. Introduction  (p. 649) | html | pdf |
    • 21.1.2. Types of error  (pp. 649-650) | html | pdf |
    • 21.1.3. Detecting outliers  (pp. 650-651) | html | pdf |
    • 21.1.4. Fixing errors  (pp. 651-652) | html | pdf |
    • 21.1.5. Preventing errors  (p. 652) | html | pdf |
    • 21.1.6. Final model  (p. 652) | html | pdf |
    • 21.1.7. A compendium of quality criteria  (pp. 652-658) | html | pdf |
    • 21.1.8. Future  (p. 658) | html | pdf |
    • References | html | pdf |
  • 21.2. Assessing the quality of macromolecular structures  (pp. 662-676) | 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. 662) | html | pdf |
    • 21.2.2. Validating the geometric and stereochemical parameters of the model  (pp. 662-665) | html | pdf |
    • 21.2.3. Validation of a model versus experimental data  (pp. 665-673) | html | pdf |
    • 21.2.4. Atomic resolution structures  (p. 673) | html | pdf |
    • 21.2.5. Concluding remarks  (p. 673) | html | pdf |
    • References | html | pdf |
  • 21.3. Detection of errors in protein models  (pp. 677-683) | html | pdf | chapter contents |
    O. Dym, D. Eisenberg and T. O. Yeates
    • 21.3.1. Motivation and introduction  (p. 677) | html | pdf |
    • 21.3.2. Separating evaluation from refinement  (p. 677) | html | pdf |
    • 21.3.3. Algorithms for the detection of errors in protein models and the types of errors they detect  (pp. 677-679) | html | pdf |
    • 21.3.4. Selection of database  (p. 679) | html | pdf |
    • 21.3.5. Examples: detection of errors in structures  (pp. 679-682) | html | pdf |
    • 21.3.6. Summary  (p. 682) | html | pdf |
    • 21.3.7. Availability of software  (p. 682) | html | pdf |
    • References | html | pdf |
  • 21.4. PROCHECK: validation of protein-structure coordinates  (pp. 684-687) | html | pdf | chapter contents |
    R. A. Laskowski, M. W. MacArthur and J. M. Thornton
    • 21.4.1. Introduction  (p. 684) | html | pdf |
    • 21.4.2. The program  (p. 684) | html | pdf |
    • 21.4.3. The parameters  (pp. 684-685) | html | pdf |
    • 21.4.4. Which parameters are best?  (p. 685) | html | pdf |
    • 21.4.5. Input  (p. 686) | html | pdf |
    • 21.4.6. Output produced  (p. 686) | html | pdf |
    • 21.4.7. Other validation tools  (p. 686) | html | pdf |
    • References | html | pdf |
  • 21.5. KiNG and kinemages  (pp. 688-693) | html | pdf | chapter contents |
    V. B. Chen, J. S. Richardson and D. C. Richardson
    • 21.5.1. Introduction to aims and concepts  (pp. 688-689) | html | pdf |
    • 21.5.2. Uses of KiNG and kinemages  (pp. 689-692) | html | pdf |
    • 21.5.3. Making kinemages  (pp. 692-693) | html | pdf |
    • 21.5.4. Software notes  (p. 693) | html | pdf |
    • References | html | pdf |
  • 21.6. MolProbity: all-atom structure validation for macromolecular crystallography  (pp. 694-701) | html | pdf | chapter contents |
    V. B. Chen, W. B. Arendall III, J. J. Headd, D. A. Keedy, R. M. Immormino, G. J. Kapral, L. W. Murray, J. S. Richardson and D. C. Richardson
    • 21.6.1. Summary of MolProbity flow and user interactions  (p. 694) | html | pdf |
    • 21.6.2. Validation analyses  (pp. 694-697) | html | pdf |
    • 21.6.3. Correction of outliers  (pp. 698-699) | html | pdf |
    • 21.6.4. Other MolProbity utility functions  (pp. 699-700) | html | pdf |
    • 21.6.5. Discussion  (p. 700) | html | pdf |
    • 21.6.6. MolProbity availability  (p. 701) | html | pdf |
    • References | html | pdf |

• Molecular geometry and features
  • 22.1. Protein geometry: volumes, areas and distances  (pp. 703-712) | html | pdf | chapter contents |
    M. Gerstein and F. M. Richards
    • 22.1.1. Introduction  (p. 703) | html | pdf |
    • 22.1.2. Definitions of protein volume  (pp. 703-706) | html | pdf |
    • 22.1.3. Definitions of protein surface  (pp. 706-708) | html | pdf |
    • 22.1.4. Definitions of atomic radii  (pp. 708-709) | html | pdf |
    • 22.1.5. Application of geometry calculations: the measurement of packing  (pp. 709-711) | html | pdf |
    • References | html | pdf |
  • 22.2. Molecular surfaces: calculations, uses and representations  (pp. 713-720) | html | pdf | chapter contents |
    M. S. Chapman and M. L. Connolly
    • 22.2.1. Introduction  (pp. 713-714) | html | pdf |
    • 22.2.2. Calculation of surface area and energies of interaction  (pp. 714-715) | html | pdf |
    • 22.2.3. Estimation of binding energies  (pp. 715-717) | html | pdf |
    • 22.2.4. Graphical representations of shape and properties  (pp. 717-719) | html | pdf |
    • 22.2.5. Conclusion  (p. 719) | html | pdf |
    • References | html | pdf |
  • 22.3. Hydrogen bonding in biological macromolecules  (pp. 721-729) | html | pdf | chapter contents |
    E. N. Baker
    • 22.3.1. Introduction  (p. 721) | html | pdf |
    • 22.3.2. Nature of the hydrogen bond  (p. 721) | html | pdf |
    • 22.3.3. Hydrogen-bonding groups  (pp. 721-722) | html | pdf |
    • 22.3.4. Identification of hydrogen bonds: geometrical considerations  (pp. 722-723) | html | pdf |
    • 22.3.5. Hydrogen bonding in proteins  (pp. 723-726) | html | pdf |
    • 22.3.6. Hydrogen bonding in nucleic acids  (pp. 726-727) | html | pdf |
    • 22.3.7. Non-conventional hydrogen bonds  (pp. 727-728) | html | pdf |
    • References | html | pdf |
  • 22.4. Electrostatic interactions in proteins  (pp. 730-735) | html | pdf | chapter contents |
    K. A. Sharp
    • 22.4.1. Introduction  (p. 730) | html | pdf |
    • 22.4.2. Theory  (pp. 730-732) | html | pdf |
    • 22.4.3. Applications  (pp. 732-734) | html | pdf |
    • References | html | pdf |
  • 22.5. The relevance of the Cambridge Structural Database in protein crystallography  (pp. 736-748) | html | pdf | chapter contents |
    F. H. Allen, J. C. Cole and M. L. Verdonk
    • 22.5.1. Introduction  (p. 736) | html | pdf |
    • 22.5.2. The CSD and the PDB: data acquisition and data quality  (pp. 736-737) | html | pdf |
    • 22.5.3. Structural knowledge from the CSD  (pp. 737-738) | html | pdf |
    • 22.5.4. Intramolecular geometry  (pp. 738-740) | html | pdf |
    • 22.5.5. Intermolecular data  (pp. 740-745) | html | pdf |
    • 22.5.6. Conclusion  (p. 745) | html | pdf |
    • References | html | pdf |

• Structural analysis and classification
  • 23.1. Protein-fold classification  (pp. 749-751) | html | pdf | chapter contents |
    C. Orengo and J. Thornton
    • References | html | pdf |
  • 23.2. Locating domains in three-dimensional structures  (pp. 752-754) | html | pdf | chapter contents |
    L. Holm and C. Sander
    • 23.2.1. Introduction  (p. 752) | html | pdf |
    • 23.2.2. Compactness  (p. 752) | html | pdf |
    • 23.2.3. Recurrence  (pp. 752-753) | html | pdf |
    • 23.2.4. Conclusion  (p. 753) | html | pdf |
    • References | html | pdf |
  • 23.3. Protein–ligand interactions  (pp. 755-765) | html | pdf | chapter contents |
    A. E. Hodel and F. A. Quiocho
    • 23.3.1. Introduction  (p. 755) | html | pdf |
    • 23.3.2. Protein–carbohydrate interactions  (pp. 755-756) | html | pdf |
    • 23.3.3. Metals  (pp. 756-757) | html | pdf |
    • 23.3.4. Protein–nucleic acid interactions  (pp. 757-760) | html | pdf |
    • 23.3.5. Phosphate and sulfate  (pp. 761-763) | html | pdf |
    • References | html | pdf |
  • 23.4. Nucleic acids  (pp. 766-799) | html | pdf | chapter contents |
    R. E. Dickerson
    • 23.4.1. Introduction  (p. 766) | html | pdf |
    • 23.4.2. Helix parameters  (pp. 766-773) | html | pdf |
    • 23.4.3. Comparison of A, B and Z helices  (pp. 773-779) | html | pdf |
    • 23.4.4. Sequence–structure relationships in B-DNA  (pp. 779-784) | html | pdf |
    • 23.4.5. Summary  (p. 784) | html | pdf |
    • Appendix 23.4.1. X-ray analyses of A, B and Z helices  (pp. 787-797) | html | pdf |
    • References | html | pdf |
  • 23.5. Solvent structure  (pp. 800-820) | html | pdf | chapter contents |
    C. Mattos and D. Ringe
    • 23.5.1. Introduction  (pp. 800-801) | html | pdf |
    • 23.5.2. Determination of water molecules  (pp. 801-802) | html | pdf |
    • 23.5.3. Structural features of protein–water interactions derived from database analysis  (pp. 802-808) | html | pdf |
    • 23.5.4. Water structure in groups of well studied proteins  (pp. 808-814) | html | pdf |
    • 23.5.5. The classic models: small proteins with high-resolution crystal structures  (pp. 814-815) | html | pdf |
    • 23.5.6. Water molecules as mediators of complex formation  (pp. 815-817) | html | pdf |
    • 23.5.7. Conclusions and future perspectives  (pp. 817-818) | html | pdf |
    • References | html | pdf |
  • 23.6. Halogen interactions in biomolecular crystal structures  (pp. 821-826) | html | pdf | chapter contents |
    M. J. Vallejos, P. Auffinger and P. S. Ho
    • 23.6.1. Introduction  (p. 821) | html | pdf |
    • 23.6.2. Classical treatment of halogen interactions  (pp. 821-822) | html | pdf |
    • 23.6.3. Electrostatic molecular halogen interactions  (pp. 822-825) | html | pdf |
    • 23.6.4. Concluding remarks  (p. 825) | html | pdf |
    • References | html | pdf |

• Crystallographic databases
  • 24.1. The Worldwide Protein Data Bank  (pp. 827-832) | html | pdf | chapter contents |
    H. M. Berman, K. Henrick, G. Kleywegt, H. Nakamura and J. Markley
    • 24.1.1. Introduction  (p. 827) | html | pdf |
    • 24.1.2. Data acquisition and processing  (pp. 827-829) | html | pdf |
    • 24.1.3. Data access  (pp. 829-831) | html | pdf |
    • 24.1.4. Future  (p. 831) | html | pdf |
    • References | html | pdf |
  • 24.2. The Nucleic Acid Database  (pp. 833-837) | html | pdf | chapter contents |
    B. Schneider, J. de la Cruz, S. Dutta, Z. Feng, L. Chen, J. Westbrook, H. Yang, J. Young, C. Zardecki and H. M. Berman
    • 24.2.1. Introduction  (p. 833) | html | pdf |
    • 24.2.2. Data processing and validation  (pp. 833-834) | html | pdf |
    • 24.2.3. The database  (pp. 834-835) | html | pdf |
    • 24.2.4. Distribution of information  (p. 835) | html | pdf |
    • References | html | pdf |
  • 24.3. The Biological Macromolecule Crystallization Database  (pp. 838-842) | html | pdf | chapter contents |
    D. T. Gallagher and M. Tung
    • 24.3.1. Introduction  (p. 838) | html | pdf |
    • 24.3.2. History of the BMCD  (p. 838) | html | pdf |
    • 24.3.3. BMCD data  (pp. 838-839) | html | pdf |
    • 24.3.4. Web interface  (p. 839) | html | pdf |
    • 24.3.5. Reproducing published crystallization procedures  (pp. 839-840) | html | pdf |
    • 24.3.6. Crystallization screens  (p. 840) | html | pdf |
    • 24.3.7. A general crystallization procedure  (pp. 840-841) | html | pdf |
    • 24.3.8. The future of the BMCD  (p. 841) | html | pdf |
    • References | html | pdf |

• A historical perspective
  • 25.1. How the structure of lysozyme was actually determined  (pp. 845-872) | 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
    • 25.1.1. Introduction  (p. 845) | html | pdf |
    • 25.1.2. Structure analysis at 6 Å resolution  (pp. 845-854) | html | pdf |
    • 25.1.3. Analysis of the structure at 2 Å resolution  (pp. 854-866) | html | pdf |
    • 25.1.4. Structural studies on the biological function of lysozyme  (pp. 866-871) | html | pdf |
    • References | html | pdf |