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Crystallographic Methods and Protocols pp 1–21Cite as

Introduction

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 56))

Abstract

This chapter is intended to give an overall view of the process of structure solution with some of the basic theory behind it. It is possible to skip the most mathematical section, at any rate, on a first reading. There is a bibliography at the end of this chapter that should provide further reading matter for readers at every level of crystallographic experience.

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References

  1. Eisenberg, D and Crothers, D (1979) Physical Chemistry with Applications to the Life Sciences, Benjamin-Cummings, Redwood City, CA

    Google Scholar 

  2. Bernal, J. D and Crowfoot, D (1934) Use of the centrifuge in determining the density of small crystals. Nature 134, 809,810

    Article  CAS  Google Scholar 

  3. Green, D. W Ingram, V M., and Perutz, M F (1954) The structure of haemoglobin IV Sign determination by the isomorphous replacement method. Proc Roy Soc A225, 287–307

    Google Scholar 

  4. Bricogne, G (1984) Maximum entropy and the foundations of Direct methods. Acta Cryst A40, 410–445

    CAS  Google Scholar 

  5. Bricogne, G. (1988) A Bayesian statistical theory of the phase problem I A multichannel maximum-entropy formalism for constructing generalized joint probability distributions of structure factors. Acta Cryst A44, 517–545

    CAS  Google Scholar 

  6. Bricogne, G (1991) Maximum entropy as a common statistical basis for all phase determination methods, in Crystallographic Computing 5 (Moras, D, Podjarny, A D, and Thierry, J C, eds), Oxford Umversity Press, Oxford, UK

    Google Scholar 

  7. Gilmore, C J and Bricogne, G. (1991) Maximun entropy, likelihood, and the phase problem in single crystal and powder diffraction, in Crystallographic Computing 5 (Moras, D., Podjarny, A D, and Thierry, J C., eds.), Oxford University Press, Oxford, UK

    Google Scholar 

  8. Patterson, A L (1935) A direct method for the determination of the components of interatomic distances in crystals. Z Krist 90, 517–542

    CAS  Google Scholar 

  9. Terwilliger, T. C, Kim, S-H, and Eisenberg, D. (1987) Generalized method of determining heavy-atom positions using the difference Patterson function. Acta Cryst A43, 1–5

    Google Scholar 

  10. Sheldrtck, G M (1990) Phase annealing in SHELX-90 Direct methods for larger structures. Acta Cryst A46, 467–473

    Google Scholar 

  11. Germam, G., Main, P, and Woolfson, M M (1971) The application of phase relationships to complex structures III The optimum use of phase relationships. Acta Cryst A21, 410–445

    Google Scholar 

  12. Sheldrick, G M (1991) Chapter 13, in Crystallographic Computing 5 (Moras, D, Podjarny, A D., and Thierry, J C, eds.), Oxford University Press, Oxford, UK

    Google Scholar 

  13. Jones, T A, Zou, J-Y, Cowan, S W, and Kjeldegaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst A47, 110–119

    CAS  Google Scholar 

  14. Jones, T. A and Kjeldegaard, M. (1994) Chapter 1, in From First Map to Final Model (Bailey, S, Hubbard, R, and Waller, D, eds), CCP4 Workgroup

    Google Scholar 

Bibliography Mathematical Texts

  • Arfken, G (1970) Mathematical Methods for Physicists Academic, New York

    Google Scholar 

  • Bamberg, P and Sternberg, S (1991) A Course in Mathematics for Students of Physics, vols 1 and 2 Cambridge University Press, New York.

    Google Scholar 

  • Boas, M L (1983) Mathematical Methods for the Physical Sciences Wiley, New York

    Google Scholar 

  • DuChateau, P C (1992) Advanced Math for Physicists and Engineers Harper Collins outline series, Harper Collms, New York

    Google Scholar 

  • Fitts, D. D. (1974) Vector Analysis in Chemistry McGraw Hill, New York.

    Google Scholar 

  • Hirst, D M (1994) Mathematics for Chemists Macmillan, New York. (This covers vector manipulation and Fourier transformation and is particularly recommended as an introduction)

    Google Scholar 

  • Janin, J. (1985) Chapter 5, in Methodes Biophysiques pour l’etude des Macromolecules, Hermann, Paris

    Google Scholar 

  • Margeneau, H. and Murphy, G M (1961) The Mathematics of Physics and Chemistry van Nostrand, Princeton, NJ

    Google Scholar 

  • Prince, E (1994) Mathematical Techniques in Crystallography and Maternal Science, 2nd ed, Springer Verlag, New York.

    Google Scholar 

  • Stephenson, G. (1979) Mathematical Methods for Science Students, 2nd ed., Longman, London.

    Google Scholar 

  • Stephenson, G. (1985) Worked Examples in Mathematics for Scientists and Engineers. Longman, London

    Google Scholar 

Basic Introductions

  • Dressier, D. and Potter, H (1991) Discovering Enzymes W H Freeman, New York.

    Google Scholar 

  • Matthew, C. K and van Holde, K E (1990) Biochemistry, Benjamin-Cummings, Redwood City, CA

    Google Scholar 

  • Stryer, L (1995) Biochemistry, 4th ed, W H Freeman, New York

    Google Scholar 

Short Introductions to X-Ray Structure Determination

  • Branden, C-I and Tooze, J (1991) Chapter 17, in Introduction to Protein Structure, Garland, New York

    Google Scholar 

  • Cantor, C R and Schimmel, P. R. (1980) Part II of Biophysical Chemistry, W. H Freeman, New York

    Google Scholar 

  • Eisenberg, D. and Crothers, D (1979) Chapters 16 and 17, in Physical Chemistry with Applications to the Life Sciences Benjamin-Cummings Publishing Company, Redwood City, CA. (Contains clear description of X-ray diffraction, which includes interesting short biographies of J D Bernal and J-B J Fourier.)

    Google Scholar 

  • Holmes, K C and Blow, D M (1965) Methods of Biochemical Analysts, vol 13, Wiley, New York, 113–239

    Book  Google Scholar 

  • Janin, J. (1985) Chapters 1–4, in Methodes Biophysiques pour l’etude des Macromolecules. Hermann, Paris (This is a very good introduction for the French reader)

    Google Scholar 

  • Perutz, M. (1992) Chapter 1 and Appendix 1, in Protein Structure, New Approaches to Disease and Therapy. W. H. Freeman, New York.

    Google Scholar 

  • Sawyer, L and Turner, M A (1992) Chapter 12, in Crystallization of Nucleic Acids and Proteins (Ducruix, A and Geige, R., eds), IRL, New York

    Google Scholar 

  • Stuart, D. and Jones, Y (1993) Chapter 9, in Protein Engineering (Sternberg, M, ed), IRL, New York.

    Google Scholar 

  • van Holde, E (1985) Physical Biochemistry, 2nd ed, Prentice-Hall, Englewood Cliffs, NJ

    Google Scholar 

Texts on X-Ray Structure Determination

  • Blundell, T B and Johnson, L H (1976) Protein Crystallography Academic, New York (This is an excellent, indispensible guide to the subject, although the data collection sections are now dated)

    Google Scholar 

  • Buerger, M J (1959) Vector Space Wiley, New York

    Google Scholar 

  • Buerger, M J (1976) Contemporary Crystallography McGraw Hill, New York

    Google Scholar 

  • Bunn, C W (1961) Chemical Crystallography, 2nd ed., Oxford University Press, New York

    Google Scholar 

  • Drenth, J (1994) The Principles of Protein X-ray Crystallography Springer-Verlag, New York.

    Google Scholar 

  • Dunitz, J D (1979) X-ray Analysis and the Structure of Organic Molecules Cornell University Press, Ithaca, N Y (This is a thorough treatment of small molecule crystallography)

    Google Scholar 

  • Giaccovazzo, C, Monaco, H L, and Viterbo, B (1992) Fundamentals of Crystallography Oxford University Press, New York

    Google Scholar 

  • Glazer, A M (1987) The Structure of Crystals, Adam Hilger, Bristol, UK

    Google Scholar 

  • Glusker, J P and Trueblood, K N (1985) Crystal Structure Analysis, A Primer, 2nd ed, Oxford University Press

    Google Scholar 

  • Ladd and Palmer, R (1989) X-ray structure determination A Practical Guide, 2nd ed, Wiley, New York (This is a very good on symmetry and space group derivations, covers both small-molecule and macromolecular crystallography )

    Google Scholar 

  • Lifson, H and Taylor, C A (1958) Fourier Transforms and X-ray Diffraction G Bell, London

    Google Scholar 

  • Lipson, H S. (1970) Crystals and X-rays Wykeham Publications Ltd, London (This is a clear elementary introduction )

    Google Scholar 

  • Lipson, H and Cochran, W (1957) The Determination of Crystal Structures G Bell, London

    Google Scholar 

  • McRee, D E (1993) Practical Protein Crystallography Academic, New York

    Google Scholar 

  • Rhodes, C (1993) Crystallography Made Crystal Clear A Guide for Users of Macromolecular Models Academic, New York.

    Google Scholar 

  • Sherwood, D. (1976) Crystals, X-rays and Proteins Wiley, New York (This is a very understandable treatment, which derives all the mathematical aspects of the subject)

    Google Scholar 

  • Stout, G H and Jensen, L H. (1989) X-ray Crystal Structure Determination, 2nd ed Wiley, New York (This provides good coverage of the basics of X-ray crystallography, primarily from a small-molecule perspective )

    Google Scholar 

  • Wilson, H R (1966) Diffraction of X-rays by Proteins, Nucleic Acids, and Viruses Edward Arnold, London. (This gives a description of diffraction and especially of helical diffraction by a member of the King’s College DNA group.)

    Google Scholar 

  • Woolfson, M M. (1978) An Introduction to X-ray Crystallography Cambridge University Press, Cambridge, UK. (This develops diffraction theory from a scattering theory perspective, rather than starting with the Bragg equation. It is an excellent treatment of Direct methods by a leader in the field and recommended for readers stronger in physics)

    Google Scholar 

  • Woolfson, M M (1961) Direct Methods in Crystallography, Oxford University Press, New York

    Google Scholar 

Advanced Texts

  • Dodson, G, Glusker, J P, and Sayre, D (eds.) (1981) Structural Studies on Molecules of Biological Interest Oxford University Press, New York

    Google Scholar 

  • Moras, D., Podjarny, A. D, and Thierry, J. C. (eds) (1991) Crystallographic Computing 5 Oxford University Press, New York (This is an extensive series of articles on all aspects of macromolecular structure solution )

    Google Scholar 

  • Rollett, J. S. (1965) Computing Methods in Crystallography Pergamon Press, Oxford

    Google Scholar 

  • Rossman, M G. (ed.) (1972) The Molecular Replacement Method Gordon and Breach, New York

    Google Scholar 

  • Wyckoff, H. W, Hirs, C H W, and Timasheff, S N (eds.) (1985) Diffraction Methods for Biological Macromolecules, Methods in Enzymology, vols. 114 and 115 Academic, New York

    Google Scholar 

CCP4 Weekend Workshops

  • Helliwell, J R, Machin, P A, and Papiz, M Z (1987) Computational Aspects of Protein Crystal Data Analysis

    Google Scholar 

  • Bailey, S, Dodson, E, and Phillips, S (1988) Improving Protein Phases

    Google Scholar 

  • Goodfellow, J, Hendrick, K., and Hubbard, R (1989) Molecular Simulation and Protein Crystallography

    Google Scholar 

  • Hendrick, K, Moss, D S, and Tickle, I J (1990) Accuracy and Reliability of Macromolecular Crystal Structures

    Google Scholar 

  • Wolf, W, Evans, P R, and Leslie, A G. W (1991) Isomorphous Replacement and Anomalous Scattering

    Google Scholar 

  • Dodson, E J, Gover, S, and Wolf, W. (1992) Molecular Replacement

    Google Scholar 

  • Sawyer, L., Isaacs, N, and Bailey, S (1993) Data Collection and Processing

    Google Scholar 

  • Bailey, S, Hubbard, R, and Walter, D (1994) From First Map to Final Model

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biophysics, King’s College, London, UK

    Mark R. Sanderson

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  1. Mark R. Sanderson
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Editor information

Editors and Affiliations

  1. National Institute for Biological Standards and Control, Potters Bar, UK

    Christopher Jones  & Barbara Mulloy  & 

  2. Department of Biophysics, King’s College, London, UK

    Mark R. Sanderson

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© 1996 Humana Press Inc.

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Sanderson, M.R. (1996). Introduction. In: Jones, C., Mulloy, B., Sanderson, M.R. (eds) Crystallographic Methods and Protocols. Methods in Molecular Biology™, vol 56. Humana Press. https://doi.org/10.1385/0-89603-259-0:1

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  • DOI: https://doi.org/10.1385/0-89603-259-0:1

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-259-0

  • Online ISBN: 978-1-59259-543-3

  • eBook Packages: Springer Protocols

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