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Journal of the Optical Society of America A

Journal of the Optical Society of America A


  • Vol. 22, Iss. 7 — Jul. 1, 2005
  • pp: 1453–1459

Phasing diffraction data from a stream of hydrated proteins

Jin Song Wu and John C.H. Spence  »View Author Affiliations

JOSA A, Vol. 22, Issue 7, pp. 1453-1459 (2005)

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We consider the problem of phase determination for continuous diffraction patterns obtained from a beam of identical, aligned large molecules (such as proteins), each coated with a layer of water or vitreous ice. Many laser-aligned molecules are assumed to lie within a wide continuous x-ray beam at any instant. An iterative phasing method is developed to extract the common target structure in three dimensions from diffraction patterns of these doped ice balls. Several measurements of the diffraction intensity in reciprocal space are needed. We found iteratively two boundaries (supports) (between protein and ice and the outer iceball support) by using the charge-flipping and multiple hybrid input–output algorithms, working with multiple sets of measured data. The approach is applied to simulated data from hydrated lysozyme proteins generated by the serial crystallography method of laser-aligned protein-beam diffraction proposed by Spence and Doak [Phys. Rev. Lett. 92, 198102 (2004) ]. We consider also the effect of empty ice balls on the patterns. The algorithm can also be used to align images with different randomly chosen origins, so that the same embedded subunits overlap.

© 2005 Optical Society of America

OCIS Codes
(100.5010) Image processing : Pattern recognition
(100.5070) Image processing : Phase retrieval
(340.7440) X-ray optics : X-ray imaging

Original Manuscript: October 29, 2004
Revised Manuscript: January 12, 2005
Manuscript Accepted: January 13, 2005
Published: July 1, 2005

Jin Song Wu and John C.H. Spence, "Phasing diffraction data from a stream of hydrated proteins," J. Opt. Soc. Am. A 22, 1453-1459 (2005)

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  1. J. C. H. Spence, B. Doak, “Single molecule diffraction,” Phys. Rev. Lett. 92, 198102 (2004). [CrossRef] [PubMed]
  2. J. C. H. Spence, K. Schmidt, J. S. Wu, G. Hembree, U. Weierstall, B. Doak, P. Fromme, “Diffraction and imaging from a beam of laser-aligned proteins: resolution limits,” Acta Crystallogr. Sect. A Found. Crystallogr. 61, 237–245 (2005). [CrossRef]
  3. H. Stapelfeldt, T. Seideman, “Colloquium: aligning molecules with strong laser pulses,” Rev. Mod. Phys. 75, 543–557 (2003). [CrossRef]
  4. H. Sakai, S. Minemoto, H. Nanjo, H. Tanji, T. Suzuki, “Controlling the orientation of polar molecules with combined electrostatic and pulsed nonresonant laser fields,” Phys. Rev. Lett. 90, 083001 (2003). [CrossRef]
  5. L. S. Bartell, J. Huang, “Supercooling of water below the anomalous range near 226 K,” J. Phys. Chem. 90, 7455–7457 (1994). [CrossRef]
  6. M. Faubel, S. Schlemmer, J. P. Toennies, “A molecular-beam study of the evaporation of water from a liquid jet,” Z. Phys. D At. Mol. Clusters 10, 269–277 (1988). [CrossRef]
  7. J. M. Zuo, I. Vartanyants, M. Gao, R. Zhang, L. A. Nagahara, “Atomic resolution imaging of a carbon nanotube from diffraction intensities,” Science 300, 1419–1421 (2003). [CrossRef] [PubMed]
  8. H. He, S. Marchesini, M. Howells, U. Weierstall, G. Hembree, J. C. H. Spence, “Experimental lensless soft-x-ray imaging using iterative algorithms: phasing diffuse scattering,” Acta Crystallogr. Sect. A Found. Crystallogr. 59, 143–152 (2003). [CrossRef]
  9. S. Marchesini, H. He, H. Chapman, S. Hau-Riege, A. Noy, M. Howells, U. Weierstall, J. C. H. Spence, “X-ray image reconstruction from a diffraction pattern alone,” Phys. Rev. B 68, 140101 (2003). [CrossRef]
  10. R. W. Gerchberg, W. O. Saxton, “Practical algorithm for determination of phase from image and diffraction plane pictures,” Optik (Stuttgart) 35, 237–246 (1972).
  11. J. R. Fienup, “Phase retrieval algorithms: a comparison,” Appl. Opt. 21, 2758–2769 (1982). [CrossRef] [PubMed]
  12. J. W. Miao, C. Charalambous, J. Kirz, D. Sayre, “Extending the methodology of x-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens,” Nature (London) 400, 342–344 (1999). [CrossRef]
  13. J. Miao, D. Sayre, “On possible extensions of x-ray crystallography through diffraction-pattern oversampling,” Acta Crystallogr. Sect. A Found. Crystallogr. 56, 596–605 (2000). [CrossRef]
  14. U. Weierstall, Q. Chen, J. C. H. Spence, M. Howells, M. Isaacson, R. R. Panepucci, “Image reconstruction from electron and x-ray diffraction patterns using iterative algorithms: experiment and simulation,” Ultramicroscopy 90, 171–195 (2001). [CrossRef]
  15. G. Oszlányi, A. Sütő, “ Ab initio structure solution by charge flipping,” Acta Crystallogr. Sect. A Found. Crystallogr. 60, 134–l41 (2004). [CrossRef]
  16. J. S. Wu, J. C. H. Spence, M. O’Keeffe, T. Groy, “Application of a modified Oszlányi and Sütő Ab initio charge-flipping algorithm to experimental data,” Acta Crystallogr. Sect. A Found. Crystallogr. 60326–330 (2004). [CrossRef]
  17. J. S. Wu, U. Weierstall, J. C. H. Spence, C. T. Koch, “Iterative phase retrieval without support,” Opt. Lett. 29, 2737–2739 (2004). [CrossRef] [PubMed]
  18. M. van Heel, B. Gowen, R. Matadeen, E. V. Orlova, R. Finn, T. Pape, D. Cohen, H. Stark, R. Schmidt, M. Schatz, A. Patwardhan, “Single-particle electron cryo-microscopy: towards atomic resolution,” Q. Rev. Biophys. 33, 307–369 (2000). [CrossRef]
  19. T. Ruiz, J. L. Ranck, R. Diaz-Avalos, D. L. D. Caspar, D. J. DeRosier, “Electron diffraction of helical particles,” Ultramicroscopy 55, 383–395 (1994). [CrossRef] [PubMed]
  20. R. Diamond, “Real-space refinement of structure of hen egg-white lysozyme,” J. Mol. Biol. 82, 371–391 (1974). [CrossRef] [PubMed]
  21. S. W. Peterson, H. A. Levy, “A single-crystal neutron diffraction study of heavy ice,” Acta Crystallogr. 10, 70–76 (1957). [CrossRef]
  22. Y. Teshima, T. Ogama, “Dense packing of equal circles on a sphere by the minimum-zenith method: symmetrical arrangement,” Forma 15, 347–364 (2000).

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