Solving structure with sparse, randomly-oriented x-ray data

Cornell University, Laboratory of Atomic and Solid State Physics, Ithaca, NY, USA.
Optics Express (Impact Factor: 3.53). 06/2012; 20(12):13129-37. DOI: 10.1364/OE.20.013129
Source: PubMed

ABSTRACT Single-particle imaging experiments of biomolecules at x-ray free-electron lasers (XFELs) require processing hundreds of thousands of images that contain very few x-rays. Each low-fluence image of the diffraction pattern is produced by a single, randomly oriented particle, such as a protein. We demonstrate the feasibility of recovering structural information at these extremes using low-fluence images of a randomly oriented 2D x-ray mask. Successful reconstruction is obtained with images averaging only 2.5 photons per frame, where it seems doubtful there could be information about the state of rotation, let alone the image contrast. This is accomplished with an expectation maximization algorithm that processes the low-fluence data in aggregate, and without any prior knowledge of the object or its orientation. The versatility of the method promises, more generally, to redefine what measurement scenarios can provide useful signal.

  • [Show abstract] [Hide abstract]
    ABSTRACT: Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources. Expected final online publication date for the Annual Review of Biophysics Volume 44 is May 06, 2015. Please see for revised estimates.
    Annual Review of Biophysics 02/2015; 44(1). DOI:10.1146/annurev-biophys-060414-033813 · 12.25 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Coherent diffractive imaging with x-ray free-electron lasers (XFEL) promises high-resolution structure determination of noncrystalline objects. Randomly oriented particles are exposed to XFEL pulses for acquisition of two-dimensional (2D) diffraction snapshots. The knowledge of their orientations enables 3D imaging by multiview reconstruction, combining 2D diffraction snapshots in different orientations. Here we introduce a globally optimal algorithm that can infer these orientations. We apply it to experimental XFEL data of nanoparticles and so determine their 3D electron density.
    Physical Review E 10/2013; 88(4-1):042710. DOI:10.1103/PhysRevE.88.042710 · 2.33 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. The EMC algorithm [Loh & Elser (2009 ▶), Phys. Rev. E, 80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philipp et al. (2012 ▶), Opt. Express, 20, 13129-13137; Ayyer et al. (2014 ▶), Opt. Express, 22, 2403-2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35 kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.
    01/2015; 2(Pt 1):29-34. DOI:10.1107/S2052252514022313

Preview (2 Sources)

1 Download
Available from