Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser

Abstract

We present a proof-of-concept three-dimensional reconstruction of the giant Mimivirus particle from experimentally measured diffraction patterns from an X-ray free-electron laser. Threedimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the X-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress (EMC) algorithm and validate our result using new methods.

Expansion-maximization-compression algorithm with spherical harmonics for single particle imaging with x-ray lasers

“…When the signal-to-noise ratio is high, as expected for large biomolecules and viruses (and already shown by a recent experiment [18]), the orientation recovery problem drives predominantly the performances of reconstruction algorithms. In the sequel, we perform numerical analysis addressing the question stated previously, taking into account both orientation recovery issue and sufficient signal-to-noise ratio.…”

“…The algorithm does not assign a single molecular orientation to each pattern, but rather it estimates the probability for a diffraction pattern to be associated with a certain orientation. Recently, this algorithm has proven its feasibility with the reconstruction of Mimivirus from experimental data collected at LCLS [18]. The EMC algorithm is studied in detail in this work, with the introduction of several improvements.…”

“…We note that in recent papers [8,18], where the EMC algorithm is applied to experimental data, an update rule of the fluence in each diffraction pattern is also derived. Here we make the simplifying assumption that the fluence in each diffraction pattern is constant.…”

Future challenges for x-ray microscopy

“…In pioneering diffract-but-destroy experiments, the external shapes of a large number of carboxysomes have been classified at 18 nm resolution [38], and single particle diffractive imaging methods have been used to image the reproducible part of the structure of the giant mimivirus at 125 nm resolution [39]. These are intruiging results; however, given the scaling of scattered signals with resolution, it is not yet clear whether these approaches can be extended towards or beyond the resolution obtained in single particle cryo electron microscopy.…”

Atomistic three-dimensional coherent x-ray imaging of nonbiological systems

“…In an early XFEL experiment, 2D imaging of a mimi virus was demonstrated to 30 nm [40]. Very recently, 3D images using that data set were obtained after orientation and reconstruction [41] of a set of 2D images, at resolution of ∼125 nm [42]. The attained resolution is rather distant from the desired 3Å, highlighting the importance of understanding fundamental processes of electronic and nuclear dynamics and imaging holistically as recently reviewed [43].…”