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Single Particle X-ray Diffraction - the Present and the Future

Single Particle X-ray Diffraction - the Present and the Future. John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center. Nobel Prizes awarded to research related to the phase problem

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Single Particle X-ray Diffraction - the Present and the Future

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  1. Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center

  2. Nobel Prizes awarded to research related to the phase problem F. Zernike (Physics in 1953), “for his invention of phase contrast method”. M. F. Perutz & J. C. Kendrew (Chemistry in 1962), “for their studies of the structures of globular proteins”. D. Gabor (Physics in 1971), “for his invention and development of the holographic method”. J. Karle & H. Hauptman (Chemistry in 1985) “for their contributions to the Direct Methods”.

  3. A 200 m crystal (a = 50 Å, 4 104 unit cells) Real Reciprocal | ℱ |    

  4. A 0.1 m crystal (a = 50 Å, 20 unit cells) Real Reciprocal | ℱ |    

  5. The Essence of the Oversampling Phasing Method Real Space ℱ Reciprocal Space Bragg-peak sampling Oversampling J. Miao, D. Sayre & H. N. Chapman, J. Opt. Soc. Am. A 15, 1662 (1998).

  6. The Oversampling Phasing Method

  7. An Iterative Algorithm JJ. Fienup, Appl. Opt. 21, 2758 (1982). JJ. Miao, J. Kirz & D. Sayre, Acta Cryst. D 56, 1312 (2000).

  8. (a) A SEM image of a double-layered sample made of Ni (~2.7 x 2.5 x 1 m3) (b) A coherent diffraction pattern from (a) (the resolution at the edge is 8 nm) (c) An image reconstructed from (b) J. Miao et al., Phys. Rev. Lett. 89, 088303 (2002).

  9. The Reconstructed 3D structure The reconstructed top pattern The reconstructed bottom pattern An iso-surface rendering of the reconstructed 3D structure

  10. Direct determination of the absolute electron density of nanostructured materials I0: Measured by an X-ray photodiode I( ): Measured by a direct-illumination CCD

  11. (a) Coherent diffraction pattern from a porous silica particle (b) The reconstructed absolute electron density (c) The absoluteelectron density distribution within a 100 x 100 nm2 area

  12. Imaging Whole E. Coli Bacteria (a) Light and fluorescence microscopy images of E. Coli labeled with YFP and manganese oxide (b) A Coherent X-ray diffraction pattern from E. Coli (c) An image reconstructed from (b).

  13. Radiation damage SSolemn & Baldwin, Science 218, 229-235 (1982). Þ With picosecond pulse duration X-rays, biological specimens remain morphological unchanged to an accuracy of a few nm. NNeutze, Wouts, Spoel, Weckert & Hajdu, Nature 400, 752-757 (2000). Þ With an X-FEL of pulse leng. < 50 fs and 3 x 1012 photons focused down to a spot of ~ 0.1 m, a 2D diffraction pattern could be recorded from a biomolecule before the radiation damage manifests itself.

  14. Orientation determination Use the methods developed in cryo-EM to determine the molecular orientation based on many 2D diffraction patterns. Crowther, Phil. Trans. Roy. Soc. Lond. B. 261, 221 (1971). J. Frank, in Three-Dimensional Electron Microscopy of Macromolecular Assemblies, Academic Press (1996). Use laser fields to physically align each molecule. J. J. Larsen, K. N. Hald, Bjerre, H. Stapelfeldt & T. Seideman, Phys. Rev. Lett. 85, 2470-2473 (2000).

  15. The 3D electron density map of a rubisco molecule The active site of the molecule

  16. Procedures to Obtain Oversampled 3D Diffraction Patterns • Calculated oversampled 2D diffraction patterns from • 106 identical molecules. • Assumed that the orientation of each 2D diffraction pattern is known. • Assembled an oversampled 3D diffraction pattern from these • oversampled 2D diffraction patterns. • (iv) Added Poisson noise to the 3D diffraction pattern.

  17. One section of the oversampled 3D diffraction • Pattern with RI = 9.8% and 3x3x3 central pixels removed (b) Top view of (a)

  18. The reconstructed 3D electron density map The reconstructed active site J. Miao, K. O. Hodgson & D. Sayre, Proc. Natl. Acad. Sci. USA 98, 6641 (2001).

  19. Reconstruction of the 3D diffraction pattern obtained from 3 x 105 identical molecules with RI = 16.6% and 3 x 3 x 3 central pixels removed.

  20. (a) The active site of the molecule from PDB (b) The reconstruction with RI = 9.8% (c) The reconstruction with RI = 16.6%

  21. SSummary • A new imaging methodology (i.e. single particle diffraction) • hasbeen developed by combiningcoherent X-rays with the oversampling method. • The 2D and 3D imaging resolution of 8 nm and 50 nm • has beenachieved. • These results will pave a way for the development of atomic resolution 3D X-ray diffraction microscopy. • In combination with the X-ray free electron lasers, single particle diffraction could be used to determine the 3D structure of single biomolcules at near atomic resolution.

  22. Acknowledgements • B. Johnson & K. Hodgson, Stanford Synchrotron Radiation Lab., Stanford University • J. Kirz & D. Sayre, SUNY at Stony Brook • C. Larabell, UC San Francisco & Lawrence Berkeley National Lab. • M. LeGros, E. Anderson, Lawrence Berkeley National Lab. • B. Lai, Advanced Photon Source, Argonne National Lab. • T. Ishikawa, Y. Nishino, RIKEN/SPring-8, Japan • J. Amonette, Pacific Northwest National Lab.

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