Advertisement

Application of In Situ Diffraction in High-Throughput Structure Determination Platforms

  • Pierre Aller
  • Juan Sanchez-Weatherby
  • James Foadi
  • Graeme Winter
  • Carina M. C. Lobley
  • Danny Axford
  • Alun W. Ashton
  • Domenico Bellini
  • Jose Brandao-Neto
  • Simone Culurgioni
  • Alice Douangamath
  • Ramona Duman
  • Gwyndaf Evans
  • Stuart Fisher
  • Ralf Flaig
  • David R. Hall
  • Petra Lukacik
  • Marco Mazzorana
  • Katherine E. McAuley
  • Vitaliy Mykhaylyk
  • Robin L. Owen
  • Neil G. Paterson
  • Pierpaolo Romano
  • James Sandy
  • Thomas Sorensen
  • Frank von Delft
  • Armin Wagner
  • Anna Warren
  • Mark Williams
  • David I. Stuart
  • Martin A. Walsh
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1261)

Abstract

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

Key words

In situ crystallography High throughput Automation Ligand screening Fragment-based drug discovery Macromolecular crystallography Data collection Crystal dehydration 

References

  1. 1.
    Garman EF (2014) Developments in X-ray crystallographic structure determination of biological macromolecules. Science 343:1102–1108PubMedCrossRefGoogle Scholar
  2. 2.
    Kantardjieff KA, Rupp B (2003) Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci 12:1865–1871PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Joachimiak A (2009) High-throughput crystallography for structural genomics. Curr Opin Struct Biol 19:573–584PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Beteva A, Cipriani F, Cusack S et al (2006) High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline. Acta Crystallogr D Biol Crystallogr 62:1162–1169PubMedCrossRefGoogle Scholar
  5. 5.
    Cohen AE, Ellis PJ, Miller MD et al (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 35:720–726PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Ohana J, Jacquamet L, Joly J et al (2004) CATS: a cryogenic automated transfer system installed on the beamline FIP at ESRF. J Appl Crystallogr 37:72–77CrossRefGoogle Scholar
  7. 7.
  8. 8.
    Cipriani F, Felisaz F, Launer L et al (2006) Automation of sample mounting for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 62:1251–1259PubMedCrossRefGoogle Scholar
  9. 9.
  10. 10.
    Snell G, Cork C, Nordmeyer R et al (2004) Automated sample mounting and alignment system for biological crystallography at a synchrotron source. Structure 12:537–545PubMedCrossRefGoogle Scholar
  11. 11.
    Jacquamet L, Ohana J, Joly J et al (2004) Automated analysis of vapor diffusion crystallization drops with an X-ray beam. Structure 12:1219–1225PubMedCrossRefGoogle Scholar
  12. 12.
    Broennimann C, Eikenberry EF, Henrich B et al (2006) The PILATUS 1M detector. J Synchrotron Radiat 13:120–130PubMedCrossRefGoogle Scholar
  13. 13.
    Axford D, Owen RL, Aishima J et al (2012) In situ macromolecular crystallography using microbeams. Acta Crystallogr D Biol Crystallogr 68:592–600PubMedCrossRefGoogle Scholar
  14. 14.
    Owen RL, Axford D, Nettleship JE et al (2012) Outrunning free radicals in room-temperature macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 68:810–818PubMedCrossRefGoogle Scholar
  15. 15.
    Owen RL, Paterson N, Axford D et al (2014) Exploiting fast detectors to enter a new dimension in room-temperature crystallography. Acta Crystallogr D Biol Crystallogr 70:1248–1256PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Ren J, Wang X, Hu Z et al (2013) Picornavirus uncoating intermediate captured in atomic detail. Nat Commun 4:1929PubMedCentralPubMedGoogle Scholar
  17. 17.
    Wang X, Peng W, Ren J et al (2012) A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429PubMedCentralPubMedCrossRefGoogle Scholar
  18. 18.
    Bingel-Erlenmeyer R, Olieric V, Grimshaw JPA et al (2011) SLS crystallization platform at beamline X06DA: a fully automated pipeline enabling in situ X-ray diffraction screening. Cryst Growth Des 11:916–923CrossRefGoogle Scholar
  19. 19.
    Deller MC, Rupp B (2014) Approaches to automated protein crystal harvesting. Acta Crystallogr F Struct Biol Commun 70:133–155PubMedCrossRefGoogle Scholar
  20. 20.
    le Maire A, Gelin M, Pochet S et al (2011) In-plate protein crystallization, in situ ligand soaking and X-ray diffraction. Acta Crystallogr D Biol Crystallogr 67:747–755PubMedCrossRefGoogle Scholar
  21. 21.
    Lobley CM, Aller P, Douangamath A et al (2012) Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118. Acta Crystallogr Sect F Struct Biol Cryst Commun 68:1427–1433PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Kiefersauer R, Stetefeld J, Gomis-Ruth FX et al (1996) Protein-crystal density by volume measurement and amino-acid analysis. J Appl Crystallogr 29:311–317CrossRefGoogle Scholar
  23. 23.
    Kiefersauer R, Than ME, Dobbek H et al (2000) A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes. J Appl Crystallogr 33:1223–1230CrossRefGoogle Scholar
  24. 24.
    Bowler MW, Montgomery MG, Leslie AG, Walker JE (2006) Reproducible improvements in order and diffraction limit of crystals of bovine mitochondrial F(1)-ATPase by controlled dehydration. Acta Crystallogr D Biol Crystallogr 62:991–995PubMedCrossRefGoogle Scholar
  25. 25.
    Russi S, Juers DH, Sanchez-Weatherby J et al (2011) Inducing phase changes in crystals of macromolecules: status and perspectives for controlled crystal dehydration. J Struct Biol 175:236–243PubMedCrossRefGoogle Scholar
  26. 26.
    Sanchez-Weatherby J, Bowler MW, Huet J et al (2009) Improving diffraction by humidity control: a novel device compatible with X-ray beamlines. Acta Crystallogr D Biol Crystallogr 65:1237–1246PubMedCrossRefGoogle Scholar
  27. 27.
    Douangamath A, Aller P, Lukacik P et al (2013) Using high-throughput in situ plate screening to evaluate the effect of dehydration on protein crystals. Acta Crystallogr D Biol Crystallogr 69:920–923PubMedCrossRefGoogle Scholar
  28. 28.
    Winston PW, Bates DH (1960) Saturated solutions for the control of humidity in biological research. Ecology 41:232–237CrossRefGoogle Scholar
  29. 29.
    Ji X, Sutton G, Evans G et al (2010) How baculovirus polyhedra fit square pegs into round holes to robustly package viruses. EMBO J 29:505–514PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Giordano R, Leal RMF, Bourenkov GP et al (2012) The application of hierarchical cluster analysis to the selection of isomorphous crystals. Acta Crystallogr D Biol Crystallogr 68:649–658PubMedCrossRefGoogle Scholar
  31. 31.
    Liu Q, Dahmane T, Zhang Z et al (2012) Structures from anomalous diffraction of native biological macromolecules. Science 336:1033–1037PubMedCentralPubMedCrossRefGoogle Scholar
  32. 32.
    Winter G (2010) xia2: an expert system for macromolecular crystallography data reduction. J Appl Crystallogr 43:186–190CrossRefGoogle Scholar
  33. 33.
    Foadi J, Aller P, Alguel Y et al (2013) Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 69:1617–1632PubMedCentralPubMedCrossRefGoogle Scholar
  34. 34.
    Leslie AG (2006) The integration of macromolecular diffraction data. Acta Crystallogr D Biol Crystallogr 62:48–57PubMedCrossRefGoogle Scholar
  35. 35.
    Leslie AG, Powell HR (2007) Processing diffraction data with mosflm evolving. Methods Macromol Crystallogr 245:41–51CrossRefGoogle Scholar
  36. 36.
    Sauter NK, Grosse-Kunstleve RW, Adams PD (2004) Robust indexing for automatic data collection. J Appl Crystallogr 37:399–409PubMedCentralPubMedCrossRefGoogle Scholar
  37. 37.
    Evans PR, Murshudov GN (2013) How good are my data and what is the resolution? Acta Crystallogr D Biol Crystallogr 69:1204–1214PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Evans P (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr D Biol Crystallogr 6:282–292CrossRefGoogle Scholar
  39. 39.
    Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242PubMedCentralPubMedCrossRefGoogle Scholar
  40. 40.
    Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66:125–132PubMedCentralPubMedCrossRefGoogle Scholar
  41. 41.
  42. 42.
    Delageniere S, Brenchereau P, Launer L et al (2011) ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics 27:3186–3192PubMedCrossRefGoogle Scholar
  43. 43.
    Kabsch W (2010) Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D Biol Crystallogr 66:133–144PubMedCentralPubMedCrossRefGoogle Scholar
  44. 44.
    Brehm W, Diederichs K (2014) Breaking the indexing ambiguity in serial crystallography. Acta Crystallogr D Biol Crystallogr 70:101–109PubMedCrossRefGoogle Scholar
  45. 45.
    Chirgadze NY, Kisselman G, Qiu W et al (2012) X-CHIP: an integrated platform for high-throughput protein crystallography. In: Benedict JB (ed) Recent advances in crystallography. InTech, Rijeka, pp 87–96Google Scholar
  46. 46.
    Dhouib K, Khan MC, Pfleging W et al (2009) Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis. Lab Chip 9:1412–1421PubMedCrossRefGoogle Scholar
  47. 47.
    Gavira JA, Toh D, Lopez-Jaramillo J et al (2002) Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling. Acta Crystallogr D Biol Crystallogr 58:1147–1154PubMedCrossRefGoogle Scholar
  48. 48.
    Gerdts CJ, Elliott M, Lovell S et al (2008) The plug-based nanovolume microcapillary protein crystallization system (MPCS). Acta Crystallogr D Biol Crystallogr 64:1116–1122PubMedCentralPubMedCrossRefGoogle Scholar
  49. 49.
    Gerdts CJ, Stahl GL, Napuli A et al (2010) Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system. J Appl Crystallogr 43:1078–1083PubMedCentralPubMedCrossRefGoogle Scholar
  50. 50.
    Kisselman G, Qiu W, Romanov V et al (2011) X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr 67:533–539PubMedCentralPubMedCrossRefGoogle Scholar
  51. 51.
    May A, Fowler B, Frankel KA et al (2008) Diffraction-capable microfluidic crystallization chips for screening and structure determination. Acta Crystallogr Sect A Found Adv 64:C133–C134CrossRefGoogle Scholar
  52. 52.
    Shim JU, Cristobal G, Link DR (2007) Using microfluidics to decouple nucleation and growth of protein crystals. Cryst Growth Des 7:2192–2194PubMedCentralPubMedCrossRefGoogle Scholar
  53. 53.
    Yadav MK, Gerdts CJ, Sanishvili R et al (2005) In situ data collection and structure refinement from microcapillary protein crystallization. J Appl Crystallogr 38:900–905PubMedCentralPubMedCrossRefGoogle Scholar
  54. 54.
    Cipriani F, Rower M, Landret C et al (2012) CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films. Acta Crystallogr D Biol Crystallogr 68:1393–1399PubMedCrossRefGoogle Scholar
  55. 55.
    Mueller U, Darowski N, Fuchs MR et al (2012) Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J Synchrotron Radiat 19:442–449PubMedCentralPubMedCrossRefGoogle Scholar
  56. 56.
    Hirata K, Kawano Y, Ueno G et al (2013) Achievement of protein micro-crystallography at SPring-8 beamline BL32XU. J Phys Conf Ser 425:012002CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Pierre Aller
    • 1
  • Juan Sanchez-Weatherby
    • 1
  • James Foadi
    • 1
  • Graeme Winter
    • 1
  • Carina M. C. Lobley
    • 1
  • Danny Axford
    • 1
  • Alun W. Ashton
    • 1
  • Domenico Bellini
    • 1
  • Jose Brandao-Neto
    • 1
  • Simone Culurgioni
    • 1
  • Alice Douangamath
    • 1
  • Ramona Duman
    • 1
  • Gwyndaf Evans
    • 1
  • Stuart Fisher
    • 1
  • Ralf Flaig
    • 1
  • David R. Hall
    • 1
  • Petra Lukacik
    • 1
  • Marco Mazzorana
    • 1
  • Katherine E. McAuley
    • 1
  • Vitaliy Mykhaylyk
    • 1
  • Robin L. Owen
    • 1
  • Neil G. Paterson
    • 1
  • Pierpaolo Romano
    • 1
  • James Sandy
    • 1
  • Thomas Sorensen
    • 1
  • Frank von Delft
    • 1
  • Armin Wagner
    • 1
  • Anna Warren
    • 1
  • Mark Williams
    • 1
  • David I. Stuart
    • 1
    • 2
  • Martin A. Walsh
    • 1
  1. 1.Diamond Light Source Ltd.OxfordshireUK
  2. 2.Division of Structural BiologyUniversity of Oxford, The Henry Wellcome Building for Genomic MedicineOxfordUK

Personalised recommendations