1. Introduction

1.1 Overview. E. Arnold & M. G. Rossmann

1.2 Historical background. M. G. Rossmann

1.3 Macromolecular crystallography and medicine. W. G. J. Hol & C. L. M. J. Verlinde

1.4 Perspectives for the future

1.4.1 Gazing into the crystal ball. E. Arnold

1.4.2 Brief comments on Gazing into the crystal ball. M. G. Rossmann

2. Basic crystallography

2.1 Introduction to basic crystallography. J. Drenth

3. Techniques of molecular biology

3.1 Preparing recombinant proteins for X-ray crystallography. S. H. Hughes & A. M. Stock

4. Crystallization

4.1 General methods. R. Giegé & A. McPherson

4.2 Crystallization of membrane proteins. H. Michel

4.3 Application of protein engineering to improve crystal properties. D. R. Davies & A. Burgess Hickman

5. Crystal properties and handling

5.1 Crystal morphology, optical properties of crystals and crystal mounting. H. L. Carrell & J. P. Glusker

5.2 Crystal-density measurements. E. M. Westbrook

6. Radiation sources and optics

6.1 X-ray sources. U. W. Arndt

6.2 Neutron sources. B. P. Schoenborn & R. Knott

7. X-ray detectors

7.1 Comparison of X-ray detectors. S. M. Gruner, E. F. Eikenberry & M. W. Tate

7.2 CCD detectors. M. W. Tate, E. F. Eikenberry & S. M. Gruner

8. Synchrotron crystallography

8.1 Synchrotron-radiation instrumentation, methods and scientific utilisation. J. R. Helliwell

8.2 Laue crystallography: time-resolved studies. K. Moffat

9. Monochromatic data collection

9.1 Principles of monochromatic data collection. Z. Dauter & K. S. Wilson

10. Cryocrystallography

10.1 Introduction to cryocrystallography. H. Hope

10.2 Cryocrystallography techniques and devices. D. W. Rodgers

11. Data processing

11.1 Automatic indexing of oscillation images. M. G. Rossmann

11.2 Integration of macromolecular diffraction data. A. G. W. Leslie

11.3 Integration, scaling, space-group assignment & post refinement. W. Kabsch

11.4 DENZO & SCALEPACK. Z. Otwinowski & W. Minor

11.5 The use of partially recorded reflections for post refinement, scaling and averaging X-ray diffraction data. C. G. van Beek, R. Bolotovsky & M. G. Rossmann

12. Isomorphous replacement

12.1 The preparation of heavy-atom derivatives of protein crystals for use in multiple isomorphous replacement and anomalous scattering. D. Carvin, S. A. Islam, M. J. E. Sternberg & T. L. Blundell

12.2 Locating heavy-atom sites. M. T. Stubbs & R. Huber

13. Molecular replacement

13.1 Noncrystallographic symmetry. D. M. Blow

13.2 Rotation functions. J. Navaza

13.3 Translation functions. L. Tong

13.4 Noncrystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension. M. G. Rossmann & E. Arnold

14. Anomalous dispersion

14.1 Heavy-atom location and phase determination with single-wavelength diffraction data. B. W. Matthews

14.2 MAD and MIR

14.2.1 Multiwavelength anomalous diffraction. J. L. Smith & W. A. Hendrickson

14.2.2 Automated MAD and MIR structure solution. T. C. Terwilliger & J. Berendzen

15. Density modification and phase combination

15.1 Phase improvement by iterative density modification. K. Y. J. Zhang, K. D. Cowtan & P. Main

15.2 Model phases: probabilities, bias and maps. R. J. Read

16. Direct methods

16.1 Ab initio phasing. G. M. Sheldrick, H. A. Hauptman, C. M. Weeks, R. Miller & I. Usón

16.2 The maximum-entropy method. G. Bricogne

17. Model building and computer graphics

17.1 Around O. G. J. Kleywegt, J.-Y. Zou, M. Kjeldgaard & T. A. Jones

17.2 Molecular graphics and animation. A. J. Olson

18. Refinement

18.1 Introduction to refinement. L. F. Ten Eyck & K. D. Watenpaugh

18.2 Enhanced macromolecular refinement by simulated annealing. A. T. Brunger, P. D. Adams & L. M. Rice

18.3 Structure quality and target parameters. R. A. Engh & R. Huber

18.4 Refinement at atomic resolution. Z. Dauter, G. N. Murshudov & K. S. Wilson

18.5 Coordinate uncertainty. D. W. J. Cruickshank

19. Other experimental techniques

19.1 Neutron crystallography: methods and information content. A. A. Kossiakoff

19.2 Electron diffraction of protein crystals. W. Chiu

19.3 Small-angle X-ray scattering. H. Tsuruta & J. E. Johnson

19.4 Small-angle neutron scattering. D. M. Engelman & P. B. Moore

19.5 Fibre diffraction. R. Chandrasekaran & G. Stubbs

19.6 Electron cryomicroscopy. T. S. Baker & R. Henderson

19.7 Nuclear magnetic resonance (NMR) spectroscopy. K. Wüthrich

20. Energy calculations and molecular dynamics

20.1 Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin. U. Stocker & W. F. van Gunsteren

20.2 Molecular-dynamics simulations of biological macromolecules. C. B. Post & V. M. Dadarlat

21. Structure validation

21.1 Validation of protein crystal structures. G. J. Kleywegt

21.2 Assessing the quality of macromolecular structures. S. J. Wodak, A. A. Vagin, J. Richelle, U. Das, J. Pontius & H. M. Berman

21.3 Detection of errors in protein models. O. Dym, D. Eisenberg & T. O. Yeates

22. Molecular geometry and features

22.1 Protein surfaces and volumes: measurement and use

22.1.1 Protein geometry: volumes, areas & distances. M. Gerstein & F. M. Richards

22.1.2 Molecular surfaces: calculations, uses and representations. M. S. Chapman & M. L. Connolly

22.2 Hydrogen bonding in biological macromolecules. E. N. Baker

22.3 Electrostatic interactions in proteins. K. A. Sharp

22.4 The relevance of the Cambridge Structural Database in protein crystallography. F. H. Allen, J. C. Cole & M. L. Verdonk

23. Structural analysis and classification

23.1 Protein folds and motifs: representation, comparison and classification

23.1.1 Protein-fold classification. C. Orengo & J. M. Thornton

23.1.2 Locating domains in 3D structures. L. Holm & C. Sander

23.2 Protein-ligand interactions. A. E. Hodel & F. A. Quiocho

23.3 Nucleic acids. R. E. Dickerson

23.4 Solvent structure. C. Mattos & D. Ringe

24. Crystallographic databases

24.1 The Protein Data Bank at Brookhaven. J. L. Sussman, D. Lin, J.-S. Jiang, N. O. Manning, J. Prilusky & E. E. Abola

24.2 The Nucleic Acid Database (NDB). H. M. Berman, Z. Feng, B. Schneider, J. Westbrook & C. Zardecki

24.3 The Cambridge Structural Database (CSD). F. H. Allen & V. J. Hoy

24.4 The Biological Macromolecule Crystallization Database. G. L. Gilliland, M. Tung & J. E. Ladner

24.5 The Protein Data Bank, 1999-. H. M. Berman, J. Westbrook, Z. Feng, G. L. Gilliland, T. N. Bhat, H. Weissig, I. N.Shindyalov & P. E. Bourne

25. Macromolecular crystallography programs

25.1 Survey of programs for crystal structure determination and analysis of macromolecules. J. Ding & E. Arnold

25.2 Programs and program systems in wide use

25.2.1 PHASES. W. Furey

25.2.2 DM/DMMULTI: software for phase improvement by density modification. K. D. Cowtan, K. Y. J. Zhang & P. Main

25.2.3 The structure determination language of the Crystallography & NMR System. 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

25.2.4 The TNT refinement package. D. E. Tronrud & L. F. Ten Eyck

25.2.5 The ARP/WARP suite for automated construction and refinement of protein models. V. S. Lamzin, A. Perrakis & K. S. Wilson

25.2.6 PROCHECK: validation of protein-structure coordinates. R. A. Laskowski, M. W. MacArthur & J. M. Thornton

25.2.7 MolScript. P. J. Kraulis

25.2.8 MAGE, PROBE and kinemages. D. C. Richardson & J. S. Richardson

25.2.9 XDS. W. Kabsch

25.2.10 Macromolecular applications of SHELX. G. M. Sheldrick

26. A historical perspective

26.1 How the structure of lysozyme was actually determined. 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 & C. A. Vernon^*