Advertisement

Modern Methods for Rapid X-Ray Diffraction Data Collection from Crystals of Macromolecules

  • Elspeth F. Garman
Part of the Methods in Molecular Biology™ book series (MIMB, volume 56)

Abstract

During the last 8 years, there has been a revolution in X-ray crystallographic data-collection technology, resulting in an enormous increase in data-acquisition rates and in the range of macromolecules that can be investigated in most laboratories. Provided that the macromolecule forms crystals of reasonable size (minimum of 100 µm in the largest dimension for in-house experiments) and quality, the next step in the determination of its three-dimensional structure is to collect X-ray diffraction data. Some fairly sophisticated equipment is required for this: an X-ray generator, an X-ray detector, and a system of stepping motors (“a goniometer”) with translational slides and rotational arcs above them (“goniometer head”) on which the crystal in a glass or quartz capillary tube is usually held using plasticene and then aligned in the X-ray beam. This chapter will outline the principles of the most commonly used laboratory equipment, and give the basic steps involved in data collection and processing.

Keywords

Dead Time Detector Face Area Detector Image Plate Main Beam 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Arndt, U. W. (1986) X-ray Position-sensitive detectors. J Appl Cryst 19, 145–163CrossRefGoogle Scholar
  2. 2.
    Pflugrath, J. W. (1992) Developments in X-ray detectors. Curr Opinion Structural Biol 2, 811–815.CrossRefGoogle Scholar
  3. 3.
    Cork, C., Hamlin, R., Vernon, W., and Xuong, Ng. H. (1975) A Xenon-filled multiwire area detector for X-ray diffraction. Acta Cryst A31, 702,703Google Scholar
  4. 4.
    Hamlin, R., Cork, C., Howard, A, Nielsen, C, Vernon, W., Matthews, D., and Xuong, Ng. H. (1981) Characteristics of a flat multiwire area detector for protein crystallography. J Appl Cryst 14, 85–93.CrossRefGoogle Scholar
  5. 5.
    Hamlin, R. (1985) Multiwire area X-ray diffractometers, in Methods in Enzymology, vol. 114 (Wyckoff, H W., Hirs, C. H. W., and Timasheff, S. N, eds.), Academic, Orlando, FL, pp. 416–451.Google Scholar
  6. 6.
    Xuong, Ng. H., Sullivan, D., Nielsen, C., and Hamlin, R. (1985) Use of the multiwire area detector diffractometer as a national resource for protein crystallography. Acta Cryst B41, 267–269Google Scholar
  7. 7.
    Durbin, R M, Burns, R, Moulai, J, Metcalf, P, Freymann, D, Blum, M, Anderson, J E, Harrison, S C, and Wiley, D C (1986) Protein, DNA, and vu-us crystallography with a focused Imaging proportional counter. Science 232, 1127–1132CrossRefGoogle Scholar
  8. 8.
    Howard, A J., Gilliland, G L, Finzel, B C, and Poulos, T L, Ohlendorf, D H, and Salemme, F R. (1987) The use of an imaging proportional counter in macro-molecular crystallography. J Appl Cryst 20, 383–387CrossRefGoogle Scholar
  9. 9.
    Arndt, U W (1982) X-ray television area detectors. Nucl Instrum Methods 201, 13–20CrossRefGoogle Scholar
  10. 10.
    Arndt, U.W, and Thomas, D J (1982) High-speed single crystal television X-ray diffractometer (hardware). Nucl Instrum Methods 201, 21–25CrossRefGoogle Scholar
  11. 11.
    Miyahara, J, Takahashi, K., Amemiya, Y, Kamiya, N., and Satow, Y (1986) A new type of X-ray area detector utilising laser stimulated luminescence. Nucl Instrum Methods A246, 572–578Google Scholar
  12. 12.
    Amemiya, Y and Miyahara, J (1988) Imaging plate illuminates many fields. Nature 336, 89,90CrossRefGoogle Scholar
  13. 13.
    Hendrix, J and Lentfer, A (1988) An imaging plate scanner. EMBL Research Reports 170,171Google Scholar
  14. 14.
    Sato, M, Yamamoto, M, Imada, K, Katsube, Y, Tanaka, N, and Higashi, T (1992) A high-speed data-collection system for large-unit-cell crystals using an imaging plate as a detector. J Appl Cyst 25, 348–357CrossRefGoogle Scholar
  15. 15.
    Strauss, M G, Westbrook, E M, Naday, I, Coleman, T A, Westbrook, M L, Travis, D J, Sweet, R M., Pflugrath, J W, and Stanton, M (1991) Large aperture CCD X-ray detector for protein crystallography using a fibreoptic taper, in Charged Coupled Devices and Solid State Optical Sensors II. SPIE 1447, pp 12–27Google Scholar
  16. 16.
    Arndt, U W and Gilmore, D J (1979) X-ray television area detectors for macromolecular structural studies with synchrotron radiation sources. J Appl Cryst 12, 1–9CrossRefGoogle Scholar
  17. 17.
    Wonacott, A J (1977) Geometry of the rotation method, in The Rotation Method in Crystallography (Arndt, U W and Wonacott, A J, eds), North-Holland, Amsterdam, pp 77–103Google Scholar
  18. 18.
    Ealick, S E and Walter, R. L (1993) Synchrotron beamlines for macromolecular crystallography. Curr Opinion in Structural Biol 3, 725–736CrossRefGoogle Scholar
  19. 19.
    Hadju, J and Johnson, L N. (1990) Progress with Laue diffraction studies on protein and virus crystals. Biochemistry 29, 1669–1678CrossRefGoogle Scholar
  20. 20.
    Clifton, I J, Fulop, V, Hadfield, A, Nordlund, P, Andersson, I, and Hadju, J (1991) Macromolecular structure, function and dynamics by fast crystallography with synchrotron radiation. Nucl. Instrum. Methods A303, 476–487Google Scholar
  21. 21.
    Sobottka, S. E., Chandross, R. J, Cornick, G C., Kretsinger, R. H., and Rains, R G (1990) Design and performance of the multiwire area X-ray diffractometer at the University of Virginia. J Appl Cryst 23, 199–208CrossRefGoogle Scholar
  22. 22.
    Baru, S E., Proviz, G. I, Savinov, G. A, Sidorov, V. A, Khabakhpashev, A G., Shekhtman, L I, Shuvalov, B N., and Yasenev, M V (1983) Two-coordinate X-ray detector. Nucl Instrum Methods 208, 445–447CrossRefGoogle Scholar
  23. 23.
    Gruner, S M, Milch, J R, and Reynolds, G T. (1982) Slow-scan silicon-intensified target-TV X-ray detector for quantitive recording of weak X-ray images. Rev Sci Instrum 53(11), 1770–1778CrossRefGoogle Scholar
  24. 24.
    Kahn, R., Fourme, R, Bosshard, R., and Saintage, V. (1986) An area-detector diffractometer for the collection of high resolution and multiwavelength anomalous diffraction data in macromolecular crystallography. Nucl Instrum Methods A246, 596–603Google Scholar
  25. 25.
    Blum, M, Metcalf, P, Harrison, S C., and Wiley, D C (1987) A System for collection and on-line integration of X-ray diffraction data from a multiwire area detector. J Appl Cyst 20, 235–242.CrossRefGoogle Scholar
  26. 26.
    Howard, A. (1993) XENGEN Version 2 1 1993. Unpublished.Google Scholar
  27. 27.
    Kabsch, W (1988) Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J Appl Cryst 21, 916–924CrossRefGoogle Scholar
  28. 28.
    Kabsch, W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown cell constants. J Appl Cryst 26, 795–800.CrossRefGoogle Scholar
  29. 29.
    SAINT (1993) Siemens Area Detection Integration Software. Unpublished.Google Scholar
  30. 30.
    Klinger, A L and Kretsinger, R. H. (1989) LATTICEPATCH—an interactive graphics program to design data measurement strategies for area detectors. J Appl Cryst 22, 287–293CrossRefGoogle Scholar
  31. 31.
    Harris, M R, Fitzgibbon, M., and Hage, F. (1989) RSPACE-a reciprocal-space modelling tool. J Appl Cryst 22, 624–627CrossRefGoogle Scholar
  32. 32.
    ASTRO (1992) Area detector strategy organiser Siemens, unpublishedGoogle Scholar
  33. 33.
    Xuong, N H, Nielsen, C., Hamlin, R, and Anderson, D (1985) Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer. J Appl Cryst 18, 342–350CrossRefGoogle Scholar
  34. 34.
    Edwards, S L, Nielsen, C, and Xuong, Ng H. (1988) Screened precession method for area detectors. Acta Cryst B44, 183–187Google Scholar
  35. 35.
    Shierbeek, A. and Parlevliet, D (1991) New developments of an X-ray television detector. Nucl Instrum Methods A310, 571–575Google Scholar
  36. 36.
    Messerschmidt, A. and Pflugrath, J. W. (1987) Crystal orientation and X-ray pattern prediction routines for area-detector diffractometer systems in macromolecular crystallography. J Appl Cryst 20, 306–315.CrossRefGoogle Scholar
  37. 37.
    Sakabe, N (1991) X-ray diffraction data collection system for modern protein crystallography with a Weissenberg camera and an image plate using synchrotron radiation. Nucl. Instrum Methods Phys Res. (A)303, 448–463.Google Scholar
  38. 38.
    Stuart, D. I. and Jones, E. Y. (1993) Weissenberg data collection for macromolecular crystallography. Curr. Opmlon in Structural Biol 3, 737–740.CrossRefGoogle Scholar
  39. 39.
    Howard, A. J., Nielsen, C., and Xuong, Ng H. (1985) Software for a diffractometer with multiwire area detector, in Methods in Enzymology, vol. 114 (Wyckoff, H W., Hirs, C H. W., Timasheff, S. N., eds.), Academic, Orlando, FL, pp 452–471.Google Scholar
  40. 40.
    Thomas, D J (1989) Calibrating an area-detector diffractometer. Imaging geometry. Proc. R Sot. Lond. A425, 129–167CrossRefGoogle Scholar
  41. 41.
    Leslie, A G W. (1992) Recent changes to the MOSFLM package for processing film and image plate data. CCP4 and ESF-EACMB Newsletter on Protein Crystallography, Number 26.Google Scholar
  42. 42.
    Higashi, T. (1989) The processing of diffraction data taken on a screenless weissenberg camera for macromolecular crystallography. J Appl Cryst 22, 9–18.CrossRefGoogle Scholar
  43. 43.
    Higashi, T (1990) Auto-indexing of oscillation images. J Appl Cryst 23, 253–257CrossRefGoogle Scholar
  44. 44.
    Rossmann, M. G (1979) Processing oscillation diffraction data for very large unit cells with an automatic convolution technique and profile fitting. J Appl Cryst 12, 225–238CrossRefGoogle Scholar
  45. 45.
    Kim, S (1989) Auto-Indexing oscillation photographs. J Appl Cryst 22, 53–60CrossRefGoogle Scholar
  46. 46.
    Tanaka, I., Yao, M, Suzuki, M, Hikichi, K, Matsumoto, T, Kozasa, M, and Katayama, C (1990) An automatic diffraction data collection system with an imaging plate. J Appl Cyst 23, 334–339CrossRefGoogle Scholar
  47. 47.
    Otwinowski, Z (1993) Oscillation data reduction program, in Data Collection and Processing (Sawyer, L, Isaacs, N., and Bailey, S., eds), SERC Daresbury Laboratory, Warrington, UK, DL/SC1/R34, pp. 56–62Google Scholar
  48. 48.
    Bricogne, G (1987) The EEC cooperative programming workshop on positionsensitive detector software, in Computational Aspects of Protein Crystal Data Analysis (Helliwell, J R., Machin, P. A, and Papiz, M Z, eds), SERC Daresbury Laboratory, Warrington, UK, DL/SCl/R25, pp. 120–135Google Scholar
  49. 49.
    Kabsch, W (1988) Automatic indexing of rotation diffraction patterns. J Appl Cryst 21, 67–71CrossRefGoogle Scholar
  50. 50.
    Howard, A (1986) Autoindexing, in Proceedings of the EEC Cooperative Workshop on Position-Sensitive Detector Software (Phases I and II), LURE, Paris, May 26–June 7, 1986, pp. 89–94Google Scholar
  51. 51.
    Diamond, R (1969) Profile analysts in single crystal diffractometry. Acta Cryst A25, 43–55Google Scholar
  52. 52.
    Evans, P. R. (1993) Data reduction, in Data Collection and Processing (Sawyer, L, Isaacs, N, and Bailey, S, eds), SERC Daresbury Laboratory, Warrington, UK, DL/SCl/R34, pp 28–32Google Scholar
  53. 53.
    Derewenda, Z. and Helliwell, J. R (1989) Calibration tests and use of a Nicolet/Xentronics imaging proportional chamber mounted on a conventional source for protein crystallography. J Appl Cryst 22, 123–137CrossRefGoogle Scholar
  54. 54.
    Garman, E F (1993) Problematic data sets give up or persist? in Data Collection and Processing (Sawyer, L., Isaacs, N, and Bailey, S., eds), SERC Daresbury Laboratory, Warrington, UK, DL/SCl/R34, pp 28–32.Google Scholar
  55. 55.
    Petsko, G. A (1975) Protein crystallography at sub-zero temperatures Cryoprotective mother liquors for protein crystals. J Mol Biol 96, 381–392CrossRefGoogle Scholar
  56. 56.
    Dewan, J. C. and Tilton, R. F (1987) Greatly reduced radiation damage in ribonuclease crystals mounted on glass fibers. J Appl Cryst 20, 130–132.CrossRefGoogle Scholar
  57. 57.
    Hope, H. (1988) Cryocrystallography of biological macromolecules: a generally applicable method. Acta Cyst B44, 22–26CrossRefGoogle Scholar
  58. 58.
    Teng, T-Y. (1990) Mounting of crystals for macromolecular crystallography in a free-standing thin film. J Appl Cryst 23, 387–391CrossRefGoogle Scholar
  59. 59.
    Gamblin, S. J and Rodgers, D W (1993) Some practical details of data collection at 100K, in Data Collection and Processing (Sawyer, L, Isaacs, N., and Bailey, S, eds.), SERC Daresbury Laboratory, Warrington, UK, DL/SCl/R34, pp 28–32.Google Scholar
  60. 60.
    Mitchell, E. P and Garman, E F (1994) Flash freezing of protein crystals investigation of mosaic spread and diffraction limit with variation of cryoprotectant concentration. J Appl Cryst 27, 1070–1074CrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 1996

Authors and Affiliations

  • Elspeth F. Garman
    • 1
  1. 1.Laboratory of Molecular BiophysicsUniversity of OxfordUK

Personalised recommendations