Hostname: page-component-78c5997874-j824f Total loading time: 0 Render date: 2024-11-14T19:09:09.084Z Has data issue: false hasContentIssue false
  • English
  • Français

Frontier methods in coherent X-ray diffraction for high-resolution structure determination

Published online by Cambridge University Press:  12 December 2016

Marcus Gallagher-Jones ,
Jose A. Rodriguez  and
Jianwei Miao
Marcus Gallagher-Jones
Affiliation:
Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
Jose A. Rodriguez*
Affiliation:
Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
Jianwei Miao*
Affiliation:
Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
*
*Author for correspondence: J. A. Rodriguez and J. Miao, Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California 90095, USA. Tel.: 310-206-2645; Fax: 310-206-5668; Email: jrodriguez@mbi.ucla.edu or miao@physics.ucla.edu
*Author for correspondence: J. A. Rodriguez and J. Miao, Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California 90095, USA. Tel.: 310-206-2645; Fax: 310-206-5668; Email: jrodriguez@mbi.ucla.edu or miao@physics.ucla.edu
Get access Rights & Permissions [Opens in a new window]

Abstract

In 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.

Type
Review
Information
Quarterly Reviews of Biophysics , Volume 49 , 2016 , e20
Copyright
Copyright © Cambridge University Press 2016 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Ackermann, W., Asova, G., Ayvazyan, V., et al. (2007) Operation of a free-electron laser from the extreme ultraviolet to the water window. Nature Photonics 1, 336–342.Google Scholar
Allaria, E., Appio, R., Badano, L., et al. (2012) Highly coherent and stable pulses from the FERMI seeded free-electron laser in the extreme ultraviolet. Nature Photonics 6, 699–704.CrossRefGoogle Scholar
Amann, J., Berg, W., Blank, V., et al. (2012) Demonstration of self-seeding in a hard-X-ray free-electron laser. Nature Photonics 6, 693–698.Google Scholar
Aquila, A., Barty, A., Bostedt, C., et al. (2015) The linac coherent light source single particle imaging road map. Structural Dynamics 2, 41701.Google Scholar
Arnlund, D., Johansson, L. C., Wickstrand, C., et al. (2014) Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nature Methods 11, 923–926.Google Scholar
Ayyer, K., Yefanov, O. M., Oberthür, D., et al. (2016) Macromolecular diffractive imaging using imperfect crystals. Nature 530, 202–206.Google Scholar
Bai, X., McMullan, G. & Scheres, S. H. W. (2015) How cryo-EM is revolutionizing structural biology. Trends in Biochemical Sciences 40, 49–57.Google Scholar
Barends, T. R. M., Foucar, L., Botha, S., et al. (2014) De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505, 244–247.Google Scholar
Barends, T. R. M., Foucar, L., Shoeman, R. L., et al. (2013) Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. Acta Crystallographica Section D Biological Crystallography 69, 838–842.Google Scholar
Battaglia, M., Contarato, D., Denes, P. & Giubilato, P. (2009) Cluster imaging with a direct detection CMOS pixel sensor in Transmission Electron Microscopy. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 608, 363–365.Google Scholar
Baxter, E. L., Aguila, L., Alonso-Mori, R., et al. (2016) High-density grids for efficient data collection from multiple crystals. Acta Crystallographica Section D: Structural Biology 72, 2–11.Google Scholar
Bogan, M. J. (2013) X-ray Free Electron Lasers Motivate Bioanalytical Characterization of Protein Nanocrystals: Serial Femtosecond Crystallography. Analytical Chemistry 85, 3464–3471.Google Scholar
Bogan, M. J., Boutet, S., Barty, A., et al. (2010) Single-shot femtosecond x-ray diffraction from randomly oriented ellipsoidal nanoparticles. Physical Review Special Topics - Accelerators and Beams 13, 94701.Google Scholar
Boutet, S., Lomb, L., Williams, G. J., et al. (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science 337, 362–364.Google Scholar
Burdet, N., Shi, X., Parks, D., et al. (2015) Evaluation of partial coherence correction in X-ray ptychography. Optics Express 23, 5452.Google Scholar
Callaway, E. (2015) The revolution will not be crystallized: a new method sweeps through structural biology. Nature News 525, 172.Google Scholar
Cammarata, M., Levantino, M., Schotte, F., et al. (2008) Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering. Nature Methods 5, 881–886.Google Scholar
Chapman, H. N., Barty, A., Bogan, M. J., et al. (2006) Femtosecond diffractive imaging with a soft-X-ray free-electron laser. Nature Physics 2, 839–843.Google Scholar
Chapman, H. N., Fromme, P., Barty, A., et al. (2011) Femtosecond X-ray protein nanocrystallography. Nature 470, 73–77.Google Scholar
Chapman, H. N. & Nugent, K. A. (2010) Coherent lensless X-ray imaging. Nature Photonics 4, 833–839.CrossRefGoogle Scholar
Chen, C.-C., Miao, J., Wang, C. W. & Lee, T. K. (2007) Application of optimization technique to noncrystalline x-ray diffraction microscopy: Guided hybrid input-output method. Physical Review B 76, 64113.Google Scholar
Chen, J. P. J., Spence, J. C. H. & Millane, R. P. (2014) Direct phasing in femtosecond nanocrystallography. II. Phase retrieval. Acta Crystallographica Section A Foundations and Advances 70, 154–161.CrossRefGoogle ScholarPubMed
Cohen, A. E., Soltis, S. M., González, A., et al. (2014) Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proceedings of the National Academy of Sciences 111, 17122–17127.Google Scholar
Deng, J., Vine, D. J., Chen, S., et al. (2015) Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae. Proceedings of the National Academy of Sciences of the United States of America 112, 2314–2319.Google Scholar
Diaz, A., Malkova, B., Holler, M., et al. (2015) Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography. Journal of Structural Biology 192, 461–469.Google Scholar
Dierolf, M., Menzel, A., Thibault, P., et al. (2010) Ptychographic X-ray computed tomography at the nanoscale. Nature 467, 436–439.CrossRefGoogle ScholarPubMed
Ekeberg, T., Svenda, M., Abergel, C., et al. (2015) Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser. Physical Review Letters 114, 98102.Google Scholar
Elser, V. (2013) Direct phasing of nanocrystal diffraction. Acta Crystallographica Section A Foundations of Crystallography 69, 559–569.Google Scholar
Emma, P., Akre, R., Arthur, J., et al. (2010) First lasing and operation of an ångstrom-wavelength free-electron laser. Nature Photonics 4, 641–647.CrossRefGoogle Scholar
Eriksson, M., van der Veen, J. F. & Quitmann, C. (2014) Diffraction-limited storage rings – a window to the science of tomorrow. Journal of Synchrotron Radiation 21, 837–842.CrossRefGoogle Scholar
Fahimian, B. P., Mao, Y., Cloetens, P. & Miao, J. (2010) Low-dose x-ray phase-contrast and absorption CT using equally sloped tomography. Physics in Medicine and Biology 55, 5383–5400.CrossRefGoogle ScholarPubMed
Faulkner, H. M. L. & Rodenburg, J. M. (2004) Movable Aperture Lensless Transmission Microscopy: A Novel Phase Retrieval Algorithm. Physical Review Letters 93, 23903.Google Scholar
Feigin, L. A., Svergun, D. I. & Taylor, G. W. (1987) Principles of the Theory of X-Ray and Neutron Scattering. In Structure Analysis by Small-Angle X-Ray and Neutron Scattering (ed Taylor, G. W.), pp. 3–24. Springer US.Google Scholar
Feld, G. K. & Frank, M. (2014) Enabling membrane protein structure and dynamics with X-ray free electron lasers. Current Opinion in Structural Biology 27, 69–78.CrossRefGoogle ScholarPubMed
Feld, G. K., Heymann, M., Benner, W. H., et al. (2015) Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography. Journal of Applied Crystallography 48, 1072–1079.Google Scholar
Fenalti, G., Zatsepin, N. A., Betti, C., et al. (2015) Structural basis for bifunctional peptide recognition at human δ-opioid receptor. Nature Structural & Molecular Biology 22, 265–268.Google Scholar
Fienup, J. R. (1978) Reconstruction of an object from the modulus of its Fourier transform. Optics Letters 3, 27–29.CrossRefGoogle ScholarPubMed
Fratzl, P., Jakob, H. F., Rinnerthaler, S., Roschger, P. & Klaushofer, K. (1997) Position-Resolved Small-Angle X-ray Scattering of Complex Biological Materials. Journal of Applied Crystallography 30, 765–769.Google Scholar
Fung, R., Shneerson, V., Saldin, D. K. & Ourmazd, A. (2009) Structure from fleeting illumination of faint spinning objects in flight. Nature Physics 5, 64–67.Google Scholar
Gallagher-Jones, M., Bessho, Y., Kim, S., et al. (2014) Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging. Nature Communications 5, 3798.Google Scholar
Galli, L., Son, S.-K., Barends, T. R. M., et al. (2015) Towards phasing using high X-ray intensity. IUCrJ 2, 627–634.Google Scholar
Gerchberg, R. W. & Saxton, W. O. (1972) A practical algorithm for the determination of the phase from image and diffraction plane pictures. Optik 35, 237–246.Google Scholar
Giewekemeyer, K., Hackenberg, C., Aquila, A., et al. (2015) Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging. Biophysical Journal 109, 1986–1995.CrossRefGoogle ScholarPubMed
Giewekemeyer, K., Thibault, P., Kalbfleisch, S., et al. (2010) Quantitative biological imaging by ptychographic x-ray diffraction microscopy. Proceedings of the National Academy of Sciences of the United States of America 107, 529–534.Google Scholar
Ginn, H. M., Brewster, A. S., Hattne, J., et al. (2015) A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Acta Crystallographica Section D Biological Crystallography 71, 1400–1410.CrossRefGoogle ScholarPubMed
Grishaev, A., Ying, J., Canny, M. D., Pardi, A. & Bax, A. (2008) Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. Journal of Biomolecular NMR 42, 99–109.Google Scholar
Guinier, A. (1938) Structure of Age-Hardened Aluminium-Copper Alloys. Nature 142, 569–570.Google Scholar
Guizar-Sicairos, M., Diaz, A., Holler, M., et al. (2011) Phase tomography from x-ray coherent diffractive imaging projections. Optics express 19, 21345–21357.CrossRefGoogle ScholarPubMed
Guttman, M., Weinkam, P., Sali, A. & Lee, K. K. (2013) All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins. Structure (London, England: 1993) 21, 321–331.CrossRefGoogle ScholarPubMed
Hantke, M. F., Hasse, D., Maia, F. R. N. C., et al. (2014) High-throughput imaging of heterogeneous cell organelles with an X-ray laser. Nature Photonics 8, 943–949.Google Scholar
Hart, P., Boutet, S., Carini, G., et al. (2012) The CSPAD megapixel x-ray camera at LCLS. In SPIE p. 85040C–85040C–11. San Diego.Google Scholar
Hatsui, T. & Graafsma, H. (2015) X-ray imaging detectors for synchrotron and XFEL sources. IUCrJ 2, 371–383.CrossRefGoogle ScholarPubMed
Hattne, J., Echols, N., Tran, R., et al. (2014) Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods 11, 545–548.Google Scholar
Hémonnot, C. Y. J., Reinhardt, J., Saldanha, O., et al. (2016) X-rays Reveal the Internal Structure of Keratin Bundles in Whole Cells. ACS Nano 10, 3553–3561.Google Scholar
Hendrickson, W. A. (1991) Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51–58.Google Scholar
Henrich, B., Bergamaschi, A., Broennimann, C., et al. (2009) PILATUS: A single photon counting pixel detector for X-ray applications. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 607, 247–249.CrossRefGoogle Scholar
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. Nature Methods 11, 734–736.Google Scholar
Hooke, R. (1667) Micrographia: Or, Some Physiological Descriptions of Minute Bodies Made by Magnifying Glasses. With Observations and Inquiries Thereupon reprint. J. Allestry, printer to the Royal Society, London.Google Scholar
Howells, M. R., Beetz, T., Chapman, H. N., et al. (2009) An assessment of the resolution limitation due to radiation-damage in X-ray diffraction microscopy. Journal of Electron Spectroscopy and Related Phenomena 170, 4–12.Google Scholar
Huang, B., Bates, M. & Zhuang, X. (2009a) Super resolution fluorescence microscopy. Annual review of biochemistry 78, 993–1016.Google Scholar
Huang, X., Nelson, J., Kirz, J., et al. (2009b) Soft X-ray diffraction microscopy of a frozen hydrated yeast cell. Physical Review Letters 103, 198101.Google Scholar
Huang, X., Harder, R., Leake, S., Clark, J. & Robinson, I. (2012) Three-dimensional Bragg coherent diffraction imaging of an extended ZnO crystal. Journal of Applied Crystallography 45, 778–784.Google Scholar
Huang, X., Lauer, K., Clark, J. N., et al. (2015) Fly-scan ptychography. Scientific Reports 5, 9074.Google Scholar
Hunter, M. S., Segelke, B., Messerschmidt, M., et al. (2014) Fixed-target protein serial microcrystallography with an x-ray free electron laser. Scientific Reports 4.CrossRefGoogle ScholarPubMed
Hura, G. L., Menon, A. L., Hammel, M., et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nature Methods 6, 606–612.Google Scholar
Ishikawa, T., Aoyagi, H., Asaka, T., et al. (2012) A compact X-ray free-electron laser emitting in the sub-angstrom region. Nature Photonics 6, 540–544.CrossRefGoogle Scholar
Jensen, M. H., Toft, K. N., David, G., et al. (2010) Time-resolved SAXS measurements facilitated by online HPLC buffer exchange. Journal of Synchrotron Radiation 17, 769–773.Google Scholar
Jiang, H., Ramunno-Johnson, D., Song, C., et al. (2008) Nanoscale imaging of mineral crystals inside biological composite materials using X-ray diffraction microscopy. Physical Review Letters 100, 38103.Google Scholar
Jiang, H., Song, C., Chen, C.-C., et al. (2010) Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proceedings of the National Academy of Sciences of the United States of America 107, 11234–11239.Google Scholar
Johansson, L. C., Arnlund, D., Katona, G., et al. (2013) Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nature Communications 4, 2911.CrossRefGoogle ScholarPubMed
Jones, M. W. M., Dearnley, M. K., van Riessen, G. A., et al. (2014) Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum. Ultramicroscopy 143, 88–92.CrossRefGoogle ScholarPubMed
Jones, M. W. M., Elgass, K. D., Junker, M. D., de Jonge, M. D. & van Riessen, G. A. (2016) Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells. Scientific Reports 6, 24280.Google Scholar
de Jonge, M. D. de, Patterson, D. J. & Ryan, C. G. (eds) (2014) XRM 2014: Proceedings of the 12th International Conference on X-ray Microscopy. AIP Conference Proceedings 1696.Google Scholar
Kam, Z. (1977) Determination of Macromolecular Structure in Solution by Spatial Correlation of Scattering Fluctuations. Macromolecules 10, 927–934.CrossRefGoogle Scholar
Kameshima, T., Ono, S., Kudo, T., et al. (2014) Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments. Review of Scientific Instruments 85, 33110.Google Scholar
Kang, Y., Zhou, X. E., Gao, X., et al. (2015) Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523, 561–567.Google Scholar
Kern, J., Alonso-Mori, R., Hellmich, J., et al. (2012) Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proceedings of the National Academy of Sciences 109, 9721–9726.Google Scholar
Kern, J., Alonso-Mori, R., Tran, R., et al. (2013) Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science 340, 491–495.Google Scholar
Kern, J., Tran, R., Alonso-Mori, R., et al. (2014) Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications 5.Google Scholar
Kim, C., Kim, Y., Song, C., et al. (2014) Resolution enhancement in coherent x-ray diffraction imaging by overcoming instrumental noise. Optics Express 22, 29161.Google Scholar
Kimura, T., Joti, Y., Shibuya, A., et al. (2014) Imaging live cell in micro-liquid enclosure by X-ray laser diffraction. Nature Communications 5, 3052.Google Scholar
Kirian, R. A., Bean, R. J., Beyerlein, K. R., et al. (2015) Direct Phasing of Finite Crystals Illuminated with a Free-Electron Laser. Physical Review X 5, 11015.CrossRefGoogle Scholar
Kirian, R. A. & Chapman, H. N. (2015) Imaging of Objects by Coherent Diffraction of X-Ray FEL Pulses. In Synchrotron Light Sources and Free-Electron Lasers (eds Jaeschke, E., Khan, S., Schneider, J. R. & Hastings, J. B.), pp. 1–55. Springer International Publishing, Cham.Google Scholar
Kirian, R. A. & Saldin, D. K. (2013) Structure Determination from Disordered Ensembles of Identical Particles. Synchrotron Radiation News 26, 20–25.Google Scholar
Kirian, R. A., Schmidt, K. E., Wang, X., Doak, R. B. & Spence, J. C. H. (2011) Signal, noise, and resolution in correlated fluctuations from snapshot small-angle x-ray scattering. Physical Review E 84.Google Scholar
Kirian, R. A., Wang, X., Weierstall, U., et al. (2010) Femtosecond protein nanocrystallography—data analysis methods. Optics Express 18, 5713–5723.Google Scholar
Koch, M. H., Vachette, P. & Svergun, D. I. (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Quarterly Reviews of Biophysics 36, 147–227.Google Scholar
Konuma, T., Kimura, T., Matsumoto, S., et al. (2011) Time-resolved small-angle X-ray scattering study of the folding dynamics of barnase. Journal of Molecular Biology 405, 1284–1294.Google Scholar
Koopmann, R., Cupelli, K., Redecke, L., et al. (2012) In vivo protein crystallization opens new routes in structural biology. Nature Methods 9, 259–262.Google Scholar
Koutsioubas, A., Berthaud, A., Mangenot, S. & Pérez, J. (2013) Ab initio and all-atom modeling of detergent organization around Aquaporin-0 based on SAXS data. The Journal of Physical Chemistry. B 117, 13588–13594.Google Scholar
Kupitz, C., Basu, S., Grotjohann, I., et al. (2014) Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature 513, 261–265.Google Scholar
Lee, E., Fahimian, B. P., Iancu, C. V., et al. (2008) Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography. Journal of Structural Biology 164, 221–227.Google Scholar
Liebi, M., Georgiadis, M., Menzel, A., et al. (2015) Nanostructure surveys of macroscopic specimens by small-angle scattering tensor tomography. Nature 527, 349–352.Google Scholar
Lima, E., Diaz, A., Guizar-Sicairos, M., et al. (2013) Cryo-scanning x-ray diffraction microscopy of frozen-hydrated yeast. Journal of Microscopy 249, 1–7.Google Scholar
Lima, E., Wiegart, L., Pernot, P., et al. (2009) Cryogenic X-Ray Diffraction Microscopy for Biological Samples. Physical Review Letters 103, 198102.Google Scholar
Liu, H. & Spence, J. C. H. (2014) The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm. IUCrJ 1, 393–401.Google Scholar
Liu, W., Wacker, D., Gati, C., et al. (2013) Serial Femtosecond Crystallography of G Protein-Coupled Receptors. Science 342, 1521–1524.Google Scholar
Loh, N. D., Bogan, M. J., Elser, V., et al. (2010) Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns. Physical Review Letters 104, 225501.Google Scholar
Loh, N. D., Hampton, C. Y., Martin, A. V., et al. (2012) Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 486, 513–517.Google Scholar
Loh, N.-T. D. & Elser, V. (2009) Reconstruction algorithm for single-particle diffraction imaging experiments. Physical Review E 80, 026705.Google Scholar
Ludtke, S. J., Baldwin, P. R. & Chiu, W. (1999) EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions. Journal of Structural Biology 128, 82–97.Google Scholar
Luke, D. R. (2005) Relaxed averaged alternating reflections for diffraction imaging. Inverse Problems 21, 37.Google Scholar
Lyubimov, A. Y., Murray, T. D., Koehl, A., et al. (2015) Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Acta Crystallographica Section D: Biological Crystallography 71, 928–940.Google Scholar
Madey, J. M. J. (1971) Stimulated Emission of Bremsstrahlung in a Periodic Magnetic Field. Journal of Applied Physics 42, 1906–1913.Google Scholar
Maiden, A. M., Morrison, G. R., Kaulich, B., Gianoncelli, A. & Rodenburg, J. M. (2013) Soft X-ray spectromicroscopy using ptychography with randomly phased illumination. Nature Communications 4, 1669.Google Scholar
Maiden, A. M. & Rodenburg, J. M. (2009) An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109, 1256–1262.Google Scholar
Mancuso, A. P., Schropp, A., Reime, B., et al. (2009) Coherent-Pulse 2D Crystallography Using a Free-Electron Laser X-Ray Source. Physical Review Letters 102.CrossRefGoogle ScholarPubMed
Mancuso, A. P., Yefanov, O. M. & Vartanyants, I. A. (2010) Coherent diffractive imaging of biological samples at synchrotron and free electron laser facilities. Journal of Biotechnology 149, 229–237.Google Scholar
Marchesini, S., He, H., Chapman, H. N., et al. (2003) X-ray image reconstruction from a diffraction pattern alone. Physical Review B 68, 140101.Google Scholar
Marchesini, S., Krishnan, H., Daurer, B. J., et al. (2016) SHARP: a distributed GPU-based ptychographic solver. Journal of Applied Crystallography 49, 1245–1252.Google Scholar
Martin-Garcia, J. M., Conrad, C. E., Coe, J., Roy-Chowdhury, S. & Fromme, P. (2016) Serial femtosecond crystallography: A revolution in structural biology. Archives of Biochemistry and Biophysics 602, 32–47.Google Scholar
Miao, J., Chapman, H. N., Kirz, J., Sayre, D. & Hodgson, K. O. (2004) Taking X-ray diffraction to the limit: macromolecular structures from femtosecond X-ray pulses and diffraction microscopy of cells with synchrotron radiation. Annual Review of Biophysics and Biomolecular Structure 33, 157–176.Google Scholar
Miao, J., Charalambous, P., Kirz, J. & Sayre, D. (1999) Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens. Nature 400, 342–344.Google Scholar
Miao, J., Ercius, P. & Billinge, S. J. L. (2016) Atomic electron tomography: 3D structures without crystals. Science 353, aaf2157 (2016).Google Scholar
Miao, J., Förster, F. & Levi, O. (2005) Equally sloped tomography with oversampling reconstruction. Physical Review B 72, 52103.Google Scholar
Miao, J., Hodgson, K. O., Ishikawa, T., et al. (2003) Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction. Proceedings of the National Academy of Sciences of the United States of America 100, 110–112.Google Scholar
Miao, J., Ishikawa, T., Johnson, B., et al. (2002) High Resolution 3D X-Ray Diffraction Microscopy. Physical Review Letters 89, 88303.Google Scholar
Miao, J., Ishikawa, T., Robinson, I. K. & Murnane, M. M. (2015) Beyond crystallography: Diffractive imaging using coherent x-ray light sources. Science 348, 530–535.Google Scholar
Miao, J., Ishikawa, T., Shen, Q. & Earnest, T. (2008) Extending X-Ray Crystallography to Allow the Imaging of Noncrystalline Materials, Cells, and Single Protein Complexes. Annual Review of Physical Chemistry 59, 387–410.Google Scholar
Miao, J., Kirz, J. & Sayre, D. (2000) The oversampling phasing method. Acta Crystallographica. Section D, Biological Crystallography 56, 1312–1315.Google Scholar
Miao, J. & Sayre, D. (2000) On possible extensions of X-ray crystallography through diffraction-pattern oversampling. Acta Crystallographica. Section A, Foundations of Crystallography 56, 596–605.Google Scholar
Miao, J., Sayre, D. & Chapman, H. N. (1998) Phase retrieval from the magnitude of the Fourier transforms of nonperiodic objects. Journal of the Optical Society of America A 15, 1662.Google Scholar
Moraes, I., Evans, G., Sanchez-Weatherby, J., Newstead, S. & Stewart, P. D. S. (2014) Membrane protein structure determination — The next generation. Biochimica et Biophysica Acta (BBA) - Biomembranes 1838, 78–87.Google Scholar
Murnane, M. M. & Miao, J. (2009) Optics: Ultrafast X-ray photography. Nature 460, 1088–1090.Google Scholar
Mutzafi, M., Shechtman, Y., Eldar, Y. C., Cohen, O. & Segev, M. (2015) Sparsity-based Ankylography for Recovering 3D molecular structures from single-shot 2D scattered light intensity. Nature Communications 6, 7950.Google Scholar
Mylonas, E., Hascher, A., Bernadó, P., et al. (2008) Domain Conformation of Tau Protein Studied by Solution Small-Angle X-ray Scattering. Biochemistry 47, 10345–10353.CrossRefGoogle ScholarPubMed
Nakane, T., Song, C., Suzuki, M., et al. (2015) Native sulfur/chlorine SAD phasing for serial femtosecond crystallography. Acta Crystallographica Section D Biological Crystallography 71, 2519–2525.Google Scholar
Nam, D., Park, J., Gallagher-Jones, M., et al. (2013) Imaging fully hydrated whole cells by coherent x-ray diffraction microscopy. Physical Review Letters 110, 98103.Google Scholar
Nashed, Y. S. G., Vine, D. J., Peterka, T., et al. (2014) Parallel ptychographic reconstruction. Optics Express 22, 32082.Google Scholar
Nelson, J., Huang, X., Steinbrener, J., et al. (2010) High-resolution x-ray diffraction microscopy of specifically labeled yeast cells. Proceedings of the National Academy of Sciences of the United States of America 107, 7235–7239.Google Scholar
Neutze, R., Brändén, G. & Schertler, G. F. (2015) Membrane protein structural biology using X-ray free electron lasers. Current Opinion in Structural Biology 33, 115–125.Google Scholar
Neutze, R., Wouts, R., van der Spoel, D., Weckert, E. & Hajdu, J. (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406, 752–757.Google Scholar
Nishino, Y., Takahashi, Y., Imamoto, N., Ishikawa, T. & Maeshima, K. (2009) Three-dimensional visualization of a human chromosome using coherent X-ray diffraction. Physical Review Letters 102, 18101.Google Scholar
Osten, P. & Margrie, T. W. (2013) Mapping brain circuitry with a light microscope. Nature Methods 10, 515–523.Google Scholar
Pedrini, B., Menzel, A., Guizar-Sicairos, M., et al. (2013) Two-dimensional structure from random multiparticle X-ray scattering images using cross-correlations. Nature Communications 4, 1647.Google Scholar
Perutz, M. F. (1956) Isomorphous replacement and phase determination in non-centrosymmetric space groups. Acta Crystallographica 9, 867–873.Google Scholar
Petoukhov, M. V. & Svergun, D. I. (2005) Global Rigid Body Modeling of Macromolecular Complexes against Small-Angle Scattering Data. Biophysical Journal 89, 1237–1250.Google Scholar
Pfeifer, M. A., Williams, G. J., Vartanyants, I. A., Harder, R. & Robinson, I. K. (2006) Three-dimensional mapping of a deformation field inside a nanocrystal. Nature 442, 63–66.Google Scholar
Ponchut, C., Rigal, J. M., Clément, J., et al. (2011) MAXIPIX, a fast readout photon-counting X-ray area detector for synchrotron applications. Journal of Instrumentation 6, C01069.Google Scholar
Popmintchev, T., Chen, M.-C., Popmintchev, D., et al. (2012) Bright Coherent Ultrahigh Harmonics in the keV X-ray Regime from Mid-Infrared Femtosecond Lasers. Science 336, 1287–1291.Google Scholar
Priebe, M., Bernhardt, M., Blum, C., et al. (2014) Scanning X-Ray Nanodiffraction on Dictyostelium discoideum. Biophysical Journal 107, 2662–2673.Google Scholar
Raines, K. S., Salha, S., Sandberg, R. L., et al. (2010) Three-dimensional structure determination from a single view. Nature 463, 214–217.Google Scholar
Rambo, R. P. & Tainer, J. A. (2010) Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Current Opinion in Structural Biology 20, 128–137.Google Scholar
Rambo, R. P. & Tainer, J. A. (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496, 477–481.Google Scholar
Ravasio, A., Gauthier, D., Maia, F. R. N. C., et al. (2009) Single-shot diffractive imaging with a table-top femtosecond soft x-ray laser-harmonics source. Physical Review Letters 103, 28104.Google Scholar
Redecke, L., Nass, K., DePonte, D. P., et al. (2013) Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339, 227–230.Google Scholar
Robinson, I. K., Vartanyants, I. A., Williams, G. J., Pfeifer, M. A. & Pitney, J. A. (2001) Reconstruction of the Shapes of Gold Nanocrystals Using Coherent X-Ray Diffraction. Physical Review Letters 87, 195505.Google Scholar
Rodenburg, J. M., Hurst, A. C., Cullis, A. G., et al. (2007) Hard-X-Ray Lensless Imaging of Extended Objects. Physical Review Letters 98, 34801.Google Scholar
Rodriguez, J. A., Xu, R., Chen, C.-C., et al. (2015) Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells. IUCrJ 2, 575–583.Google Scholar
Rodriguez, J. A., Xu, R., Chen, C.-C., Zou, Y. & Miao, J. (2013) Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities. Journal of Applied Crystallography 46, 312–318.Google Scholar
Roessler, C. G., Kuczewski, A., Stearns, R., et al. (2013) Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines. Journal of Synchrotron Radiation 20, 805–808.Google Scholar
Rossmann, M. G. & Blow, D. M. (1962) The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallographica 15, 24–31.Google Scholar
Saldin, D. K., Poon, H. C., Shneerson, V. L., et al. (2010) Beyond small-angle x-ray scattering: Exploiting angular correlations. Physical Review B 81, 174105.Google Scholar
Sandberg, R. L., Paul, A., Raymondson, D., et al. (2007) Lensless diffractive imaging using tabletop, coherent, high harmonic soft X-ray beams. Physical Review Letters 99, 098103.Google Scholar
Sandberg, R. L., Song, C., Wachulak, P. W., et al. (2008) High numerical aperture tabletop soft x-ray diffraction microscopy with 70-nm resolution. Proceedings of the National Academy of Sciences of the United States of America 105, 24–27.Google Scholar
Santi, P. A. (2011) Light Sheet Fluorescence Microscopy A Review. Journal of Histochemistry & Cytochemistry 59, 129–138.Google Scholar
Sawaya, M. R., Cascio, D., Gingery, M., et al. (2014) Protein crystal structure obtained at 2·9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proceedings of the National Academy of Sciences 111, 12769–12774.Google Scholar
Sayre, D. (1952) Some implications of a theorem due to Shannon. Acta Crystallographica 5, 843–843.CrossRefGoogle Scholar
Sayre, D. (1980) Prospects for long-wavelength X-ray microscopy and diffraction. In Imaging Processes and Coherence in Physics (eds Schlenker, M., Fink, M., Goedgebuer, J. P., et al. ), pp. 229–235. Springer Berlin Heidelberg.Google Scholar
Schaff, F., Bech, M., Zaslansky, P., et al. (2015) Six-dimensional real and reciprocal space small-angle X-ray scattering tomography. Nature 527, 353–356.Google Scholar
Schlichting, I. (2015) Serial femtosecond crystallography: the first five years. IUCrJ 2, 246–255.Google Scholar
Schlichting, I. & Miao, J. (2012) Emerging opportunities in structural biology with X-ray free-electron lasers. Current Opinion in Structural Biology 22, 613–626.Google Scholar
van der Schot, G., Svenda, M., Maia, F. R. N. C., et al. (2015) Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nature Communications 6, 5704.Google Scholar
Schroer, C. G., Kuhlmann, M., Roth, S. V., et al. (2006) Mapping the local nanostructure inside a specimen by tomographic small-angle x-ray scattering. Applied Physics Letters 88, 164102.Google Scholar
Seaberg, M. D., Adams, D. E., Townsend, E. L., et al. (2011) Ultrahigh 22 nm resolution coherent diffractive imaging using a desktop 13 nm high harmonic source. Optics Express 19, 22470–22479.Google Scholar
Seibert, M. M., Ekeberg, T., Maia, F. R. N. C., et al. (2011) Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470, 78–81.Google Scholar
Shapiro, D., Thibault, P., Beetz, T., et al. (2005) Biological imaging by soft x-ray diffraction microscopy. Proceedings of the National Academy of Sciences of the United States of America 102, 15343–15346.Google Scholar
Shapiro, D. A., Yu, Y.-S., Tyliszczak, T., et al. (2014) Chemical composition mapping with nanometre resolution by soft X-ray microscopy. Nature Photonics 8, 765–769.Google Scholar
Shechtman, Y., Eldar, Y. C., Cohen, O., et al. (2015) Phase Retrieval with Application to Optical Imaging: A contemporary overview. IEEE Signal Processing Magazine 32, 87–109.Google Scholar
Shen, Q., Bazarov, I. & Thibault, P. (2004) Diffractive imaging of nonperiodic materials with future coherent X-ray sources. Journal of Synchrotron Radiation 11, 432–438.Google Scholar
Sherrell, D. A., Foster, A. J., Hudson, L., et al. (2015) A modular and compact portable mini-endstation for high-precision, high-speed fixed target serial crystallography at FEL and synchrotron sources. Journal of Synchrotron Radiation 22, 1372–1378.Google Scholar
Sierra, R. G., Laksmono, H., Kern, J., et al. (2012) Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallographica Section D: Biological Crystallography 68, 1584–1587.Google Scholar
Solem, J. C. (1986) Imaging biological specimens with high-intensity soft x rays. JOSA B 3, 1551–1565.Google Scholar
Song, C., Jiang, H., Mancuso, A., et al. (2008) Quantitative imaging of single, unstained viruses with coherent x rays. Physical Review Letters 101, 158101.Google Scholar
Song, C., Takagi, M., Park, J., et al. (2014) Analytic 3D imaging of mammalian nucleus at nanoscale using coherent x-rays and optical fluorescence microscopy. Biophysical Journal 107, 1074–1081.Google Scholar
Spence, J. C. H., Kirian, R. A., Wang, X., et al. (2011) Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals. Optics Express 19, 2866–2873.CrossRefGoogle ScholarPubMed
Spence, J. C. H., Weierstall, U. & Chapman, H. N. (2012) X-ray lasers for structural and dynamic biology. Reports on Progress in Physics 75, 102601.Google Scholar
Starodub, D., Aquila, A., Bajt, S., et al. (2012) Single-particle structure determination by correlations of snapshot X-ray diffraction patterns. Nature Communications 3, 1276.Google Scholar
Strüder, L., Epp, S., Rolles, D., et al. (2010) Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 614, 483–496.Google Scholar
Sugahara, M., Mizohata, E., Nango, E., et al. (2014) Grease matrix as a versatile carrier of proteins for serial crystallography. Nature Methods 12, 61–63.Google Scholar
Svergun, D. I., Petoukhov, M. V. & Koch, M. H. (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophysical journal 80, 2946–2953.Google Scholar
Takahashi, Y., Suzuki, A., Furutaku, S., et al. (2013) Bragg x-ray ptychography of a silicon crystal: Visualization of the dislocation strain field and the production of a vortex beam. Physical Review B 87, 121201.Google Scholar
Takayama, Y., Maki-Yonekura, S., Oroguchi, T., Nakasako, M. & Yonekura, K. (2015) Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects. Scientific Reports 5, 8074.Google Scholar
Thibault, P., Dierolf, M., Bunk, O., Menzel, A. & Pfeiffer, F. (2009) Probe retrieval in ptychographic coherent diffractive imaging. Ultramicroscopy 109, 338–343.Google Scholar
Thibault, P., Dierolf, M., Menzel, A., et al. (2008) High-resolution scanning x-ray diffraction microscopy. Science (New York, N.Y.) 321, 379–382.CrossRefGoogle ScholarPubMed
Thibault, P. & Guizar-Sicairos, M. (2012) Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14, 63004.Google Scholar
Thibault, P. & Menzel, A. (2013) Reconstructing state mixtures from diffraction measurements. Nature 494, 68–71.Google Scholar
Uervirojnangkoorn, M., Zeldin, O. B., Lyubimov, A. Y., et al. (2015) Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. eLife 4.Google Scholar
Usón, I. & Sheldrick, G. M. (1999) Advances in direct methods for protein crystallography. Current Opinion in Structural Biology 9, 643–648.Google Scholar
Watanabe, S., Punge, A., Hollopeter, G., et al. (2011) Protein localization in electron micrographs using fluorescence nanoscopy. Nature Methods 8, 80–84.Google Scholar
Weierstall, U., James, D., Wang, C., et al. (2014) Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nature Communications 5.Google Scholar
Weierstall, U., Spence, J. C. H. & Doak, R. B. (2012) Injector for scattering measurements on fully solvated biospecies. Review of Scientific Instruments 83, 35108.Google Scholar
Weinhausen, B., Nolting, J.-F., Olendrowitz, C., et al. (2012) X-ray nano-diffraction on cytoskeletal networks. New Journal of Physics 14, 85013.Google Scholar
Weinhausen, B., Saldanha, O., Wilke, R. N., et al. (2014) Scanning X-Ray Nanodiffraction on Living Eukaryotic Cells in Microfluidic Environments. Physical Review Letters 112, 88102.Google Scholar
Westenhoff, S., Malmerberg, E., Arnlund, D., et al. (2010) Rapid readout detector captures protein time-resolved WAXS. Nature Methods 7, 775–776.Google Scholar
White, T. A., Kirian, R. A., Martin, A. V., et al. (2012) CrystFEL: a software suite for snapshot serial crystallography. Journal of Applied Crystallography 45, 335–341.Google Scholar
Wilke, R. N., Priebe, M., Bartels, M., et al. (2012) Hard X-ray imaging of bacterial cells: nano-diffraction and ptychographic reconstruction. Optics Express 20, 19232–19254.Google Scholar
Wright, G. S. A., Hasnain, S. S. & Grossmann, J. G. (2011) The structural plasticity of the human copper chaperone for SOD1: insights from combined size-exclusion chromatographic and solution X-ray scattering studies. Biochemical Journal 439, 39–44.Google Scholar
Xu, R., Jiang, H., Song, C., et al. (2014) Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nature Communications 5, 4061.Google Scholar
Xu, R., Salha, S., Raines, K. S., et al. (2011) Coherent diffraction microscopy at SPring-8: instrumentation, data acquisition and data analysis. Journal of Synchrotron Radiation 18, 293–298.Google Scholar
Yamashita, K., Pan, D., Okuda, T., et al. (2015) An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Scientific Reports 5, 14017.Google Scholar
Yu, C.-J., Lee, H. C., Kim, C., et al. (2014) Coherent X-ray scattering beamline at port 9C of Pohang Light Source II. Journal of Synchrotron Radiation 21, 264–267.Google Scholar
Zanette, I., Enders, B., Dierolf, M., et al. (2015) Ptychographic X-ray nanotomography quantifies mineral distributions in human dentine. Scientific Reports 5, 9210.Google Scholar
Zhang, H., Unal, H., Gati, C., et al. (2015) Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography. Cell 161, 833–844.Google Scholar