Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Giegé R (2013) A historical perspective on protein crystallization from 1840 to the present day. FEBS J 280:6456–6497
Bernal JD, Crowfoot D (1934) X-ray photographs of crystalline pepsin. Nature 133:794–795
Phillips JC, Wlodawer A, Yevitz MM et al (1976) Applications of synchrotron radiation to protein crystallography: preliminary results. Proc Natl Acad Sci U S A 73:128–132
Riekel C (2004) Recent developments in microdiffraction on protein crystals. J Synchrotron Radiat 11:4–6
Nelson R, Sawaya MR, Balbirnie M et al (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435:773–777
Moukhametzianov R, Burghammer M, Edwards PC et al (2008) Protein crystallography with a micrometre-sized synchrotron-radiation beam. Acta Crystallogr D Biol Crystallogr 64:158–166
Sanishvili R, Yoder DW, Pothineni SB et al (2011) Radiation damage in protein crystals is reduced with a micron-sized X-ray beam. Proc Natl Acad Sci U S A 108:6127–6132
Chapman HN, Fromme P, Barty A et al (2011) Femtosecond X-ray protein nanocrystallography. Nature 470:73–77
Sanishvili R, Nagarajan V, Yoder D et al (2008) A 7 microm mini-beam improves diffraction data from small or imperfect crystals of macromolecules. Acta Crystallogr D Biol Crystallogr 64:425–435
Fischetti RF, Xu S, Yoder DW et al (2009) Mini-beam collimator enables microcrystallography experiments on standard beamlines. J Synchrotron Radiat 16:217–225
Henderson R (1995) The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q Rev Biophys 28:171–193
Petsko GA (1975) Protein crystallography at sub-zero temperatures: cryo-protective mother liquors for protein crystals. J Mol Biol 96:381–392
Teng T-Y (1990) Mounting of crystals for macromolecular crystallography in a free-standing thin film. J Appl Crystallogr 23:387–391
Hope H (1990) Crystallography of biological macromolecules at ultra-low temperature. Annu Rev Biophys Biophys Chem 19:107–126
Axford D, Owen RL, Aishima J et al (2012) In situ macromolecular crystallography using microbeams. Acta Crystallogr D Biol Crystallogr 68:592–600
Landau EM, Rosenbusch JP (1996) Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A 93:14532–14535
Caffrey M (2015) A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. Acta Crystallogr F Struct Biol Commun 71:3–18
Rodriguez JA, Ivanova MI, Sawaya MR et al (2015) Structure of the toxic core of α-synuclein from invisible crystals. Nature 525:486–490
Stevenson HP, Makhov AM, Calero M et al (2014) Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proc Natl Acad Sci U S A 111:8470–8475
Perrakis A, Cipriani F, Castagna J-C et al (1999) Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13. Acta Crystallogr D Biol Crystallogr 55:1765–1770
Fuchs MR, Pradervand C, Thominet V et al (2014) D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source. J Synchrotron Radiat 21:340–351
Khan I, Gillilan R, Kriksunov I et al (2012) Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning. J Appl Crystallogr 45:936–943
Gilis D, Massar S, Cerf NJ et al (2001) Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2:1–12
Lunde CS, Rouhani S, Remis JP et al (2005) UV microscopy at 280 nm is effective in screening for the growth of protein microcrystals. J Appl Crystallogr 38:1031–1034
Gill H (2010) Evaluating the efficacy of tryptophan fluorescence and absorbance as a selection tool for identifying protein crystals. Acta Crystallogr F Struct Biol Commun 66:364–372
Calero G, Cohen AE, Luft JR et al (2014) Identifying, studying and making good use of macromolecular crystals. Acta Crystallogr F Struct Biol Commun 70:993–1008
Chavas LMG, Yamada Y, Hiraki M et al (2011) UV LED lighting for automated crystal centring. J Synchrotron Radiat 18:11–15
Ravelli RBG, Leiros H-KS, Pan B et al (2003) Specific radiation damage can be used to solve macromolecular crystal structures. Structure 11:217–224
de Sanctis D, Zubieta C, Felisaz F et al (2016) Radiation-damage-induced phasing: a case study using UV irradiation with light-emitting diodes. Acta Crystallogr D Biol Crystallogr 72:395–402
Snell EH, van der Woerd MJ, Miller MD et al (2005) Finding a cold needle in a warm haystack: infrared imaging applied to locating cryocooled crystals in loops. J Appl Crystallogr 38:69–77
Newman JA, Zhang S, Sullivan SZ et al (2016) Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging. J Synchrotron Radiat 23:959–965
Glassford SE, Byrne B, Kazarian SG (2013) Recent applications of ATR FTIR spectroscopy and imaging to proteins. Biochim Biophys Acta 1834:2849–2858
Echalier A, Glazer RL, Fulop V et al (2004) Assessing crystallization droplets using birefringence. Acta Crystallogr D Biol Crystallogr 60:696–702
Eftink MR (1991) Fluorescence techniques for studying protein structure. In: Suelter CH (ed) Methods of biochemical analysis: protein structure determination, vol 35. John Wiley & Sons, Inc., New York, pp 127–205
Callis PR, Vivian JT (2003) Understanding the variable fluorescence quantum yield of tryptophan in proteins using QM-MM simulations. Quenching by charge transfer to the peptide backbone. Chem Phys Lett 369:409–414
Judge RA, Swift K, Gonzalez C (2005) An ultraviolet fluorescence-based method for identifying and distinguishing protein crystals. Acta Crystallogr D Biol Crystallogr 61:60–66
Desbois S, Seabrook SA, Newman J (2013) Some practical guidelines for UV imaging in the protein crystallization laboratory. Acta Crystallogr F Struct Biol Commun 69:201–208
Ediger MD, Moog RS, Boxer SG et al (1982) On the refractive index correction in luminescence spectroscopy. Chem Phys Lett 88:123–127
Pohl E, Ristau U, Gehrmann T et al (2004) Automation of the EMBL Hamburg protein crystallography beamline BW7B. J Synchrotron Radiat 11:372–377
Vernede X, Lavault B, Ohana J et al (2006) UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops. Acta Crystallogr D Biol Crystallogr 62:253–261
Gofron KJ, Duke NEC (2011) Using X-ray excited UV fluorescence for biological crystal location. Nucl Instrum Methods A 649:216–218
Madden JT, DeWalt EL, Simpson GJ (2011) Two-photon excited UV fluorescence for protein crystal detection. Acta Crystallogr D Biol Crystallogr 67:839–846
Madden JT, Toth SJ, Dettmar CM et al (2013) Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline. J Synchrotron Radiat 20:531–540
Shukla A, Mukherjee S, Sharma S et al (2004) A novel UV laser-induced visible blue radiation from protein crystals and aggregates: scattering artifacts or fluorescence transitions of peptide electrons delocalized through hydrogen bonding? Arch Biochem Biophys 428:144–153
Lukk T, Gillilan RE, Szebenyi DME et al (2016) A visible-light-excited fluorescence method for imaging protein crystals without added dyes. J Appl Crystallogr 49:234–240
Sumner JB, Dounce AL (1937) Crystalline catalase. Science 85:366–367
Meyer A, Betzel C, Pusey M (2015) Latest methods of fluorescence-based protein crystal identification. Acta Crystallogr F Struct Biol Commun 71:121–131
Groves MR, Muller IB, Kreplin X et al (2007) A method for the general identification of protein crystals in crystallization experiments using a noncovalent fluorescent dye. Acta Crystallogr D Biol Crystallogr 63:526–535
Watts D, Muller-Dieckmann J, Tsakanova G et al (2010) Quantitive evaluation of macromolecular crystallization experiments using 1,8-ANS fluorescence. Acta Crystallogr D Biol Crystallogr 66:901–908
Forsythe E, Achari A, Pusey ML (2006) Trace fluorescent labeling for high-throughput crystallography. Acta Crystallogr D Biol Crystallogr 62:339–346
Pusey M, Barcena J, Morris M et al (2015) Trace fluorescent labeling for protein crystallization. Acta Crystallogr F Struct Biol Commun 71:806–814
Suzuki N, Hiraki M, Yamada Y et al (2010) Crystallization of small proteins assisted by green fluorescent protein. Acta Crystallogr D Biol Crystallogr 66:1059–1066
Karain WI, Bourenkov GP, Blume H et al (2002) Automated mounting, centering and screening of crystals for high-throughput protein crystallography. Acta Crystallogr D Biol Crystallogr 58:1519–1522
Stepanov S, Hilgart M, Yoder D et al (2011) Fast fluorescence techniques for crystallography beamlines. J Appl Crystallogr 44:772–778
Wampler RD, Kissick DJ, Dehen CJ et al (2008) Selective detection of protein crystals by second harmonic microscopy. J Am Chem Soc 130:14076–14077
Kissick DJ, Dettmar CM, Becker M et al (2013) Towards protein-crystal centering using second-harmonic generation (SHG) microscopy. Acta Crystallogr D Biol Crystallogr 69:843–851
Moad AJ, Moad CW, Perry JM et al (2007) NLOPredict: visualization and data analysis software for nonlinear optics. J Comput Chem 28:1996–2002
Haupert LM, DeWalt EL, Simpson GJ (2012) Modeling the SHG activities of diverse protein crystals. Acta Crystallogr D Biol Crystallogr 68:1513–1521
Haupert L, Simpson G (2011) Screening of protein crystallization trials by second order nonlinear optical imaging of chiral crystals (SONICC). Methods 55:379–386
Kissick DJ, Gualtieri EJ, Simpson GJ et al (2010) Nonlinear optical imaging of integral membrane protein crystals in lipidic mesophases. Anal Chem 82:491–497
DeWalt EL, Begue VJ, Ronau JA et al (2013) Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains. Acta Crystallogr D Biol Crystallogr 69:74–81
Closser RG, Gualtieri EJ, Newman JA et al (2013) Characterization of salt interferences in second-harmonic generation detection of protein crystals. J Appl Crystallogr 46:1903–1906
Newman JA, Scarborough NM, Pogranichniy NR et al (2015) Intercalating dyes for enhanced contrast in second-harmonic generation imaging of protein crystals. Acta Crystallogr D Biol Crystallogr 71:1471–1477
Dettmar CM, Newman JA, Toth SJ et al (2015) Imaging local electric fields produced upon synchrotron X-ray exposure. Proc Natl Acad Sci U S A 112:696–701
Song J, Mathew D, Jacob SA et al (2007) Diffraction-based automated crystal centering. J Synchrotron Radiat 14:191–195
Cherezov V, Hanson MA, Griffith MT et al (2009) Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 micron size X-ray synchrotron beam. J R Soc Interface 6(Suppl 5):S587–S597
Bowler MW, Guijarro M, Petitdemange S et al (2010) Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection. Acta Crystallogr D Biol Crystallogr 66:855–864
Aishima J, Owen RL, Axford D et al (2010) High-speed crystal detection and characterization using a fast-readout detector. Acta Crystallogr D Biol Crystallogr 66:1032–1035
Hilgart MC, Sanishvili R, Ogata CM et al (2011) Automated sample-scanning methods for radiation damage mitigation and diffraction-based centering of macromolecular crystals. J Synchrotron Radiat 18:717–722
Stevenson HP, Lin G, Barnes CO et al (2016) Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Biol Crystallogr 72:603–615
Shi D, Nannenga BL, de la Cruz MJ et al (2016) The collection of MicroED data for macromolecular crystallography. Nat Protoc 11:895–904
Shi D, Nannenga BL, Iadanza MG et al (2013) Three-dimensional electron crystallography of protein microcrystals. elife 2:e01345
Rodriguez JA, Gonen T (2016) High-resolution macromolecular structure determination by MicroED, a cryo-EM method. Methods Enzymol 579:369–392
Warren AJ, Armour W, Axford D et al (2013) Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging. Acta Crystallogr D Biol Crystallogr 69:1252–1259
Nishizawa N, Ishida S, Hirose M et al (2012) Three-dimensional, non-invasive, cross-sectional imaging of protein crystals using ultrahigh resolution optical coherence tomography. Biomed Opt Express 3:735–740
Nitahara S, Maeki M, Yamaguchi H et al (2012) Three-dimensional Raman spectroscopic imaging of protein crystals deposited on a nanodroplet. Analyst 137:5730–5735
Owen RL, Juanhuix J, Fuchs M (2016) Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 602:21–31
Kawabata K, Takahashi M, Saitoh K et al (2006) Evaluation of crystalline objects in crystallizing protein droplets based on line-segment information in greyscale images. Acta Crystallogr D Biol Crystallogr 62:239–245
Pan S, Shavit G, Penas-Centeno M et al (2006) Automated classification of protein crystallization images using support vector machines with scale-invariant texture and Gabor features. Acta Crystallogr D Biol Crystallogr 62:271–279
Lavault B, Ravelli RBG, Cipriani F (2006) C3D: a program for the automated centring of cryocooled crystals. Acta Crystallogr D Biol Crystallogr 62:1348–1357
Pothineni SB, Strutz T, Lamzin VS (2006) Automated detection and centring of cryocooled protein crystals. Acta Crystallogr D Biol Crystallogr 62:1358–1368
Sullivan SZ, Muir RD, Newman JA et al (2014) High frame-rate multichannel beam-scanning microscopy based on Lissajous trajectories. Opt Express 22:24224–24234
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
Yamada Y, Hiraki M, Matsugaki N et al (2016) In-situ data collection at the photon factory macromolecular crystallography beamlines. AIP Conf Proc 1741:050023
Huang C-Y, Olieric V, Ma P et al (2015) In meso in situ serial X-ray crystallography of soluble and membrane proteins. Acta Crystallogr D Biol Crystallogr 71:1238–1256
Huang C-Y, Olieric V, Ma P et al (2016) In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Acta Crystallogr D Biol Crystallogr 72:93–112
Murray TD, Lyubimov AY, Ogata CM et al (2015) A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. Acta Crystallogr D Biol Crystallogr 71:1987–1997
Lyubimov AY, Murray TD, Koehl A et al (2015) Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Acta Crystallogr D Biol Crystallogr 71:928–940
Roedig P, Vartiainen I, Duman R et al (2015) A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering. Sci Rep 5:10451
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
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
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
Baxter EL, Aguila L, Alonso-Mori R et al (2016) High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Biol Crystallogr 72:2–11
Maeki M, Pawate AS, Yamashita K et al (2015) A method of cryoprotection for protein crystallography by using a microfluidic chip and its application for in situ X-ray diffraction measurements. Anal Chem 87:4194–4200
Pawate AS, Srajer V, Schieferstein J et al (2015) Towards time-resolved serial crystallography in a microfluidic device. Acta Crystallogr F Struct Biol Commun 71:823–830
Sui S, Wang Y, Kolewe KW et al (2016) Graphene-based microfluidics for serial crystallography. Lab Chip 16:3082–3096
Axford D, Foadi J, Hu N-J et al (2015) Structure determination of an integral membrane protein at room temperature from crystals in situ. Acta Crystallogr D Biol Crystallogr 71:1228–1237
Boutet S, Lomb L, Williams GJ et al (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science 337:362–364
DePonte DP, Weierstall U, Schmidt K et al (2008) Gas dynamic virtual nozzle for generation of microscopic droplet streams. J Phys D 41:195505
Johansson LC, Arnlund D, White TA et al (2012) Lipidic phase membrane protein serial femtosecond crystallography. Nat Methods 9:263–265
Sierra RG, Laksmono H, Kern J et al (2012) Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallogr D Biol Crystallogr 68:1584–1587
Liu W, Wacker D, Gati C et al (2013) Serial femtosecond crystallography of G protein-coupled receptors. Science 342:1521–1524
Stellato F, Oberthur D, Liang M et al (2014) Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCrJ 1:204–212
Gati C, Bourenkov G, Klinge M et al (2014) Serial crystallography on in vivo grown microcrystals using synchrotron radiation. IUCrJ 1:87–94
Roessler CG, Agarwal R, Allaire M et al (2016) Acoustic injectors for drop-on-demand serial femtosecond crystallography. Structure 24:631–640
Nannenga BL, Shi D, Leslie AGW et al (2014) High-resolution structure determination by continuous-rotation data collection in MicroED. Nat Methods 11:927–930
Stevens A, Kovarik L, Abellan P et al (2015) Applying compressive sensing to TEM video: a substantial frame rate increase on any camera. Adv Struct Chem Imaging 1:1–20
Kiefersauer R, Grandl B, Krapp S et al (2014) IR laser-induced protein crystal transformation. Acta Crystallogr D Biol Crystallogr 70:1224–1232
Cheng Y (2015) Single-particle cryo-EM at crystallographic resolution. Cell 161:450–457
Becker M, Weckert E (2012) On the possibility of determining structures of membrane proteins in two-dimensional crystals using X-ray free electron lasers. In: Cheng RH, Hammar L (eds) Conformational proteomics of macromolecular architecture. World Scientific, Singapore, pp 133–147
Hirata K, Shinzawa-Itoh K, Yano N et al (2014) Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Nat Methods 11:734–736
Cohen AE, Soltis SM, González A et al (2014) Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A 111:17122–17127
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Becker, M., Kissick, D.J., Ogata, C.M. (2017). Locating and Visualizing Crystals for X-Ray Diffraction Experiments. In: Wlodawer, A., Dauter, Z., Jaskolski, M. (eds) Protein Crystallography. Methods in Molecular Biology, vol 1607. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7000-1_6
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7000-1_6
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6998-2
Online ISBN: 978-1-4939-7000-1
eBook Packages: Springer Protocols