Skip to main content
SpringerLink
Log in

X-Ray Sources and High-Throughput Data Collection Methods

  • Protocol
  • First Online:
Structure-Based Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 841))

  • 2723 Accesses

Abstract

X-ray diffraction experiments on protein crystals are at the core of the structure determination process. An overview of X-ray sources and data collection methods to support structure-based drug design (SBDD) efforts is presented in this chapter. First, methods of generating and manipulating X-rays for the purpose of protein crystallography, as well as the components of the diffraction experiment setup are discussed. SBDD requires the determination of numerous protein–ligand complex structures in a timely manner, and the second part of this chapter describes how to perform diffraction experiments efficiently on a large number of crystals, including crystal screening and data collection.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

     Å stands for Ångstrom, which is a widely used unit of X-ray wavelength, 1 Å  =  0.1 nm  =  100 pm.

References

  1. Hoffman, I., Protein Crystallization for Structure Based Drug Design, in this book.

    Google Scholar 

  2. Drenth, J. (2006) Principles of Protein X-Ray Crystallography. Springer.

    Google Scholar 

  3. Ogata, C. (2009) Private communications.

    Google Scholar 

  4. http://www.rigaku.com/generators/fre-plus.html

  5. http://hyperphysics.phy-astr.gsu.edu/hbase/quantum/xrayc.html; Image reproduced with permission from R. Nave (2010)

  6. http://henke.lbl.gov/optical_constants/bend2.html

  7. http://radiant.harima.riken.go.jp/spectra/index.html

  8. Elder, F. R., Gurewitsch, A. M., Langmuir, R. V., and Pollock, H. C. (1947) Radiation from Electrons in a Synchrotron. Phys. Rev. 71, 829–830.

    Article  CAS  Google Scholar 

  9. http://en.wikipedia.org/wiki/X-ray_tube

  10. Kwiatkowski, W., Noel, J. P., and Choe, S. (2000) Use of Cr K α radiation to enhance the signal from anomalous scatterers including sulfur. J. Appl. Cryst. 33, 876–881.

    Article  CAS  Google Scholar 

  11. Watanabe, N. (2006) From phasing to structure refinement in-house: Cr/Cu dual-wavelength system and a loopless free crystal-mounting method. Acta Cryst. D62, 891–896.

    CAS  Google Scholar 

  12. http://www.rigaku.com/protein/phasing.html

  13. Robin, D. et al (2005) Superbend upgrade on the Advanced Light Source. Nucl. Instrum. Methods A538, 65–92.

    Google Scholar 

  14. Robin, D. (2009) Private communications.

    Google Scholar 

  15. X-RAY DATA BOOKLET (2009), Center for X-ray Optics and Advanced Light Source, Lawrence Berkeley National Laboratory. 3rd ed.

    Google Scholar 

  16. Ruth, R. (2010) Private communications and http://www.lynceantech.com

  17. Miao, J., Ishikawa, T., Shen, Q., and Earnest, T. (2008) Extending X-ray crystallography to allow the imaging of noncrystalline materials, cells, and single protein complexes. Annu. Rev. Phys. Chem. 59, 387–410.

    Article  PubMed  CAS  Google Scholar 

  18. Henke B. L., Gullikson E. M., and Davis J. C. (1993). X-ray interactions: photoabsorption, scattering, transmission, and reflection at E = 50-30000 eV, Z = 1–92. Atomic Data and Nuclear Data Tables 54, 181–342, and http://henke.lbl.gov/optical_constants/

  19. Morton, S. (2010) Private communications.

    Google Scholar 

  20. Deutsch, M., Förster, E., Hölzer, G., Härtwig, J., Hämäläinen, K., Kao, C.-C., Huotari, D., and Diamant, R. (2004) X-Ray Spectrometry of Copper: New Results on an Old Subject. J. Res. Natl. Inst. Stand. Technol. 109, 75–98.

    Article  CAS  Google Scholar 

  21. Miller, M. (2009) Private communications and http://www.px.nsls.bnl.gov/x12c/CCM-description.html

  22. Underwood, J. H. (2009) in X-RAY DATA BOOKLET, Center for X-ray Optics and Advanced Light Source, Lawrence Berkeley National Laboratory. 3rd ed., Section 4–1

    Google Scholar 

  23. http://henke.lbl.gov/cgi-bin/mldata.pl

  24. Padmore, H. A., Earnest, T., Kim, S.-H., Thompson, A. C., and Robinson, A. L. (1995) A beamline for macromolecular crystallography at the Advanced Light Source. Rev. Sci. Instrum. 66, 1738–1740.

    Article  CAS  Google Scholar 

  25. Earnest, T., Padmore, H., Cork, C., Behrsing, R., and Kim, S. H. (1996) The macromolecular crystallography facility at the advanced light source. J. Cryst. Growth 168, 248–252.

    Article  CAS  Google Scholar 

  26. Morton, S. et al (2007) Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines. Synchrotron Rad. News, 20, 2330.

    Article  Google Scholar 

  27. http://www.biosync.rcsb.org

  28. Helliwell, J. R. (1992) Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press.

    Google Scholar 

  29. Snell, G., Cork, C., Nordmeyer, R., Cornell, E., Meigs, G., Yegian, D., Jaklevic, J., Jin, J., Stevens, R. C., and Earnest, T. (2004) Automated sample mounting and alignment system for biological crystallography at a synchrotron source. Structure 12, 537–45.

    Article  PubMed  CAS  Google Scholar 

  30. Fischetti, R. F., Xu, S., Yoder, D. W., Becker, M., Nagarajan, V., Sanishvili, R., Hilgart, M. C., Stepanov, S., Makarov, O., and Smith, J. L. (2009) Mini-beam collimator enables microcrystallography experiments on standard beamlines. J. Synchrotron Radiat. 16, 217–25.

    Article  PubMed  CAS  Google Scholar 

  31. Ellis, P. J., Cohen, A. E. & Soltis, S. M. (2003) Beamstop with integrated X-ray sensor. J. Synchrotron Rad. 10, 287–288.

    Article  Google Scholar 

  32. Muchmore, S. W., Olson, J., Jones, R., Pan, J., Blum, M., Greer, J.,Merrick, S. M., Magdalinos, P., and Nienaber, V. L. (2000) Automated crystal mounting and data collection for protein crystallography. Structure 8, R243-R246.

    Article  PubMed  CAS  Google Scholar 

  33. Cohen, A.E., Ellis, P.J., Miller, M.D., Deacon, A.M., and Phizackerley, R.P. (2002) An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot. J. Appl. Crystallogr. 35, 720–726.

    Article  CAS  Google Scholar 

  34. http://smb.slac.stanford.edu/robosync/

  35. http://www.adsc-xray.com

  36. http://www.mar-usa.com

  37. http://www.dectris.com

  38. Rupp, B., Segelke, B. W., Krupka, H. I., Lekin, T.P., Schafer, J., Zemla, A., Toppani, D., Snell, G., and Earnest, T. (2002) The TB structural genomics consortium crystallization facility: toward automation from protein to electron density. Acta Crystallogr. D58, 1514–1518.

    CAS  Google Scholar 

  39. Stevens, R.C., Yokoyama, S., and Wilson, I.A. (2001) Global efforts in structural genomics. Science 294, 89–92.

    Article  PubMed  CAS  Google Scholar 

  40. Scapin, G., (2006) Structural biology and drug discovery. Curr. Pharm. Des. 12, 2087–97.

    Article  PubMed  CAS  Google Scholar 

  41. Santarsiero B. D., Yegian D. T., Lee C. C., Spraggon G., Gu J., Scheibe D., Uber D. C., Cornell E. W., Nordmeyer R. A., Kolbe W. F., Jin J., Jones A. L., Jaklevic J. M., Schultz P. G., and Stevens R. C. (2002) An approach to rapid protein crystallization using nanodroplets. J. Appl. Cryst. 35, 278–281.

    Article  CAS  Google Scholar 

  42. Hosfield D., Palan J., Hilgers M., Scheibe D., McRee D. E., and Stevens R. C. (2003) A fully integrated protein crystallization platform for small-molecule drug discovery. J Struct Biol. 142, 207–17.

    Article  PubMed  CAS  Google Scholar 

  43. Carter, D. C., Rhodes, P., McRee, D. E., Tari, L. W., Dougan, D. R., Snell, G., Abola, E., and Stevens, R. C. (2005) Reduction in diffuso-convective disturbances in nanovolume protein crystallization experiments. J. Appl. Cryst. 38, 87–90.

    Article  CAS  Google Scholar 

  44. Nowakowski J., Cronin C. N., McRee D. E., Knuth M. W., Nelson C. G., Pavletich N. P., Rogers J., Sang B. C., Scheibe D. N., Swanson R. V., and Thompson D. A. (2002) Structures of the cancer-related Aurora-A, FAK, and EphA2 protein kinases from nanovolume crystallography. Structure 10, 1659–67.

    Article  PubMed  CAS  Google Scholar 

  45. Mol C. D., Dougan D. R., Schneider T. R., Skene R. J., Kraus M. L., Scheibe D. N., Snell G. P., Zou H., Sang B. C., and Wilson K. P. (2004) Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J. Biol. Chem. 279, 31655–63.

    Article  PubMed  CAS  Google Scholar 

  46. Aertgeerts K., Ye S., Tennant M. G., Kraus M. L., Rogers J., Sang B. C., Skene R. J., Webb D. R., and Prasad G. S. (2004) Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation. Protein Sci., 13, 412–21.

    Article  PubMed  CAS  Google Scholar 

  47. Somoza J. R., Skene R. J., Katz B. A., Mol C., Ho J. D., Jennings A. J., Luong C., Arvai A., Buggy J. J., Chi E., Tang J., Sang B. C., Verner E., Wynands R., Leahy E. M., Dougan D. R., Snell G., Navre M., Knuth M. W., Swanson R. V., McRee D. E., and Tari L. W. (2004) Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure 12, 1325–34.

    Article  PubMed  CAS  Google Scholar 

  48. Hosfield D. J., Wu Y., Skene R. J., Hilgers M., Jennings A., Snell G. P., and Aertgeerts K. (2005) Conformational flexibility in crystal structures of human 11beta-hydroxysteroid dehydrogenase type I provide insights into glucocorticoid interconversion and enzyme regulation. J. Biol. Chem. 280, 4639–48.

    Article  PubMed  CAS  Google Scholar 

  49. Aertgeerts K., Levin I., Shi L., Snell G. P., Jennings A., Prasad G. S., Zhang Y., Kraus M. L., Salakian S., Sridhar V., Wijnands R., and Tennant M. G. (2005) Structural and kinetic analysis of the substrate specificity of human fibroblast activation protein alpha. J. Biol. Chem. 280, 19441–19444.

    Article  PubMed  CAS  Google Scholar 

  50. Fujimoto T., Imaeda Y., Konishi N., Hiroe K., Kawamura M., Textor G. P., Aertgeerts K., and Kubo K. (2010) Discovery of a tetrahydropyrimidin-2(1H)-one derivative (TAK-442) as a potent, selective, and orally active factor Xa inhibitor. J. Med. Chem. 53, 3517–31.

    Article  PubMed  CAS  Google Scholar 

  51. Feng J., Zhang Z., Wallace M. B., Stafford J. A., Kaldor S. W., Kassel D. B., Navre M., Shi L., Skene R. J., Asakawa T., Takeuchi K., Xu R., Webb D. R., and Gwaltney S. L. (2007) Discovery of alogliptin: a potent, selective, bioavailable, and efficacious inhibitor of dipeptidyl peptidase IV. J Med Chem. 50, 2297–300.

    Article  PubMed  CAS  Google Scholar 

  52. Karain, W. I., Bourenkov, G. P., Blume, H, and Bartunik, H. D. (2002) Automated mounting, centering and screening of crystals for high-throughput protein crystallography. Acta Crystallogr. D58, 1519–22.

    CAS  Google Scholar 

  53. Song, J., Mathew, D., Jacob, S. A., Corbett, L., Moorhead, and P., Soltis, S. M. (2007) Diffraction-based automated crystal centering. J Synchrotron Radiat. 14, 191–195.

    Google Scholar 

  54. Jain, A., and Stojanoff, V. (2007) Are you centered? An automatic crystal-centering method for high-throughput macromolecular crystallography. J Synchrotron Radiat. 14, 355–60.

    Article  PubMed  CAS  Google Scholar 

  55. http://www.scripps.edu/~arvai/adxv.html

  56. Sauter, N. K., Grosse-Kunstleve, R. W., and Adams, P. D. (2004). J. Appl. Cryst. 37, 399–409.

    Google Scholar 

  57. Zhang, Z., Sauter, N. K., van den Bedem, H., Snell, G., and Deacon, A. M. (2006). J. Appl. Cryst. 39, 112–119.

    Google Scholar 

  58. Dauter, Z., (2005) Efficient use of synchrotron radiation for macromolecular diffraction data collection. Progess in Biophysics and Molecular Biology 89, 153–172.

    Article  CAS  Google Scholar 

  59. Holton, J. M. (2009) A beginner’s guide to radiation damage. J Synchrotron Radiat. 16, 133–42.

    Article  PubMed  CAS  Google Scholar 

  60. Holton, J. M. (2008) Expected crystal lifetimes at synchrotron beamlines. http://bl831.als.lbl.gov/damage_rates.pdf

  61. Popov, A. N., and Bourenkov, G. P. (2003) Choice of data-collection parameters based on statistic modeling. Acta Cryst. D59, 1145–1153.

    CAS  Google Scholar 

  62. Ravelli, R. B. G., Sweet, R. M., Skinner, J. M., Duisenberg, A. J. M., and Kroon, J. (1997) STRATEGY: a program to optimize the starting spindle angle and scan range for X-ray data collection. J. Appl. Cryst. 30, 551–554.

    Article  CAS  Google Scholar 

  63. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol. 276, 307–326.

    Article  CAS  Google Scholar 

  64. Leslie, G. W., (2006) The integration of macromolecular diffraction data. Acta Cryst. D62, 48–57.

    CAS  Google Scholar 

  65. Pflugrath, J. W., (1999) The finer things in X-ray diffraction data collection. Acta Cryst. D55, 1718–1725.

    CAS  Google Scholar 

  66. Diederich, K., and Karplus, A., (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Structural Biology 4, 269–274.

    Article  Google Scholar 

  67. Weiss, M.S., Global indicators of X-ray data quality. J. Appl. Cryst. 34, 130–135 (2001).

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This chapter is dedicated to Peter Boyd of Boyd Technologies, whose invaluable contributions to sample handling automation at synchrotron facilities helped to realize high-throughput SBDD.

The majority of the work described in this chapter has been performed at beamline 5.0.3 of the Advanced Light Source, in Berkeley, CA. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231. ALS beamline 5.0.3 has been constructed and is being operated by the Berkeley Center for Structural Biology (BCSB). Contributions by former and current members of the BCSB are greatly appreciated.

The work presented in this chapter has been carried out as part of the TSD high-throughput SBDD efforts, which were made possible by the members of the structural biology department.

Portions of the data have been collected at the Advanced Photon Source (APS) GM/CA CAT beamlines, beamline X6A of National Synchrotron Light Source (NSLS), and the structural biology beamlines of SSRL. Use of the APS was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. GM/CA CAT has been funded in whole or in part with Federal funds from the National Cancer Institute (Y1-CO-1020) and the National Institute of General Medical Science (Y1-GM-1104). The SSRL is a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences. Beam line X6A is funded by the National Institute of General Medical Sciences, National Institute of Health under agreement GM-0080. Use of the National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

I would like to thank Scott W. Lane (TSD) for careful reading of the manuscript and for the many helpful suggestions. I would also like to thank Simon A. Morton (LBNL) for fruitful discussions and help with the wiggler and undulator spectral distribution calculations.

Author information

Authors and Affiliations

  1. Takeda San Diego, San Diego, CA, USA

    Gyorgy Snell

Authors
  1. Gyorgy Snell
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gyorgy Snell .

Editor information

Editors and Affiliations

  1. Trius Therapeutics, Nancy Ridge Dr. 6310, San Diego, 92121, California, USA

    Leslie W. Tari

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Snell, G. (2012). X-Ray Sources and High-Throughput Data Collection Methods. In: Tari, L. (eds) Structure-Based Drug Discovery. Methods in Molecular Biology, vol 841. Humana Press. https://doi.org/10.1007/978-1-61779-520-6_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-520-6_5

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-519-0

  • Online ISBN: 978-1-61779-520-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation