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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Garman EF (2014) Developments in X-ray crystallographic structure determination of biological macromolecules. Science 343:1102–1108
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 12:1865–1871
Joachimiak A (2009) High-throughput crystallography for structural genomics. Curr Opin Struct Biol 19:573–584
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 62:1162–1169
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 35:720–726
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 37:72–77
Cipriani F, Felisaz F, Launer L et al (2006) Automation of sample mounting for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 62:1251–1259
Snell G, Cork C, Nordmeyer R et al (2004) Automated sample mounting and alignment system for biological crystallography at a synchrotron source. Structure 12:537–545
Jacquamet L, Ohana J, Joly J et al (2004) Automated analysis of vapor diffusion crystallization drops with an X-ray beam. Structure 12:1219–1225
Broennimann C, Eikenberry EF, Henrich B et al (2006) The PILATUS 1M detector. J Synchrotron Radiat 13:120–130
Axford D, Owen RL, Aishima J et al (2012) In situ macromolecular crystallography using microbeams. Acta Crystallogr D Biol Crystallogr 68:592–600
Owen RL, Axford D, Nettleship JE et al (2012) Outrunning free radicals in room-temperature macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 68:810–818
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 70:1248–1256
Ren J, Wang X, Hu Z et al (2013) Picornavirus uncoating intermediate captured in atomic detail. Nat Commun 4:1929
Wang X, Peng W, Ren J et al (2012) A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429
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 11:916–923
Deller MC, Rupp B (2014) Approaches to automated protein crystal harvesting. Acta Crystallogr F Struct Biol Commun 70:133–155
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 67:747–755
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 68:1427–1433
Kiefersauer R, Stetefeld J, Gomis-Ruth FX et al (1996) Protein-crystal density by volume measurement and amino-acid analysis. J Appl Crystallogr 29:311–317
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 33:1223–1230
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 62:991–995
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 175:236–243
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 65:1237–1246
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 69:920–923
Winston PW, Bates DH (1960) Saturated solutions for the control of humidity in biological research. Ecology 41:232–237
Ji X, Sutton G, Evans G et al (2010) How baculovirus polyhedra fit square pegs into round holes to robustly package viruses. EMBO J 29:505–514
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 68:649–658
Liu Q, Dahmane T, Zhang Z et al (2012) Structures from anomalous diffraction of native biological macromolecules. Science 336:1033–1037
Winter G (2010) xia2: an expert system for macromolecular crystallography data reduction. J Appl Crystallogr 43:186–190
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 69:1617–1632
Leslie AG (2006) The integration of macromolecular diffraction data. Acta Crystallogr D Biol Crystallogr 62:48–57
Leslie AG, Powell HR (2007) Processing diffraction data with mosflm evolving. Methods Macromol Crystallogr 245:41–51
Sauter NK, Grosse-Kunstleve RW, Adams PD (2004) Robust indexing for automatic data collection. J Appl Crystallogr 37:399–409
Evans PR, Murshudov GN (2013) How good are my data and what is the resolution? Acta Crystallogr D Biol Crystallogr 69:1204–1214
Evans P (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr D Biol Crystallogr 6:282–292
Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242
Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66:125–132
Delageniere S, Brenchereau P, Launer L et al (2011) ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics 27:3186–3192
Kabsch W (2010) Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D Biol Crystallogr 66:133–144
Brehm W, Diederichs K (2014) Breaking the indexing ambiguity in serial crystallography. Acta Crystallogr D Biol Crystallogr 70:101–109
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 87–96
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 9:1412–1421
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 58:1147–1154
Gerdts CJ, Elliott M, Lovell S et al (2008) The plug-based nanovolume microcapillary protein crystallization system (MPCS). Acta Crystallogr D Biol Crystallogr 64:1116–1122
Gerdts CJ, Stahl GL, Napuli A et al (2010) Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system. J Appl Crystallogr 43:1078–1083
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 67:533–539
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–C134
Shim JU, Cristobal G, Link DR (2007) Using microfluidics to decouple nucleation and growth of protein crystals. Cryst Growth Des 7:2192–2194
Yadav MK, Gerdts CJ, Sanishvili R et al (2005) In situ data collection and structure refinement from microcapillary protein crystallization. J Appl Crystallogr 38:900–905
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 68:1393–1399
Mueller U, Darowski N, Fuchs MR et al (2012) Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J Synchrotron Radiat 19:442–449
Hirata K, Kawano Y, Ueno G et al (2013) Achievement of protein micro-crystallography at SPring-8 beamline BL32XU. J Phys Conf Ser 425:012002
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Aller, P. et al. (2015). Application of In Situ Diffraction in High-Throughput Structure Determination Platforms. In: Owens, R. (eds) Structural Proteomics. Methods in Molecular Biology, vol 1261. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2230-7_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2230-7_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2229-1
Online ISBN: 978-1-4939-2230-7
eBook Packages: Springer Protocols