Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

Abstract

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns

“…The diffraction pattern sets were converted to have log values while performing the search such that the rotational masked correlation coefficient, CC, 18 is defined as…”

“…For three-dimensional (3D) reconstruction of the structure, a large number of diffraction patterns of homogeneous samples need to be collected and then assembled to create a 3D map. There are a few current methods, such as slice matching; the expand, maximize, and compress (EMC) algorithm; and other maximum likelihood approaches. − The estimated amount of data required to achieve resolutions of 10 Å run in thousands of patterns, depending on experimental conditions and samples. ,, However, such data collection is still very challenging, and the data being produced is limited. Therefore, it is useful to have a tool that can infer 3D biomolecular structure information even from XFEL data that are in smaller quantities or lower resolutions.…”

Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching

“…To determine the orientation angles of the samples against the incident beam captured in each diffraction pattern, we performed slice matching [34]. We used annular regions on the diffraction patterns defined by the inner and outer radii, R i and R o , for slice matching, and set these parameters corresponding to the same wavenumber among the diffraction beam intensity in this study.…”

Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments

“…One group of methods to orient the diffraction patterns in SPI relies on the information in the common intersection curves of the patterns (Huldt et al, 2003;Shneerson et al, 2008;Bortel & Tegze, 2011;Yefanov & Vartanyants, 2013;Zhou et al, 2014). Other methods find the possible orientations of the patterns by comparing them with a 3D intensity model updated by every iteration (Loh & Elser, 2009;Tegze & Bortel, 2012;Flamant et al, 2016;Nakano et al, 2017Nakano et al, , 2018. Another group of methods uses the manifold embedding technique to find the similarities between diffraction patterns and order them in the orientation space (Fung et al, 2009;Giannakis et al, 2012;Kassemeyer et al, 2013;Winter et al, 2016).…”