Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination.

Xuanxuan Li,John C H Spence,Haiguang Liu,Brenda G Hogue

doi:10.1107/s2052252517012398

Xuanxuan Li, John C H Spence + Show 2 more

Open Access

https://doi.org/10.1107/s2052252517012398

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Abstract

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core-shell architecture were used as a model system for proof-of-principle coherent diffractive single-particle imaging experiments. To deal with the heterogeneity of the core-shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core-shell architecture.

Highlights

The realization of the ‘diffraction-before-destruction’ experimental approach at X-ray free electron laser (XFEL) facilities, such as the Linac Coherent Light Source (LCLS) at SLAC National Laboratory (Menlo Park, California, USA), makes it possible to outrun radiation damage (Chapman et al, 2006) using ultrashort X-ray pulses (Emma et al, 2010)
There are successful cases demonstrating the application of these algorithms in handling heterogeneous sample data, where Kassemeyer et al (2013) used the geodesic and in-plane rotations algorithm (GIPRAL) to select the Coherent diffraction imaging (CDI) data that correspond to the same sized particles
We focused mainly on the results obtained using this reference model to investigate the orientation distribution and size variation of the nanoparticles that were intercepted by XFEL pulses

Summary

Introduction

The realization of the ‘diffraction-before-destruction’ experimental approach at X-ray free electron laser (XFEL) facilities, such as the Linac Coherent Light Source (LCLS) at SLAC National Laboratory (Menlo Park, California, USA), makes it possible to outrun radiation damage (Chapman et al, 2006) using ultrashort X-ray pulses (Emma et al, 2010). The manifold embedding method maps each scattering pattern onto the SO(3) rotation space, based on the assumption that similar patterns, represented by a vector in higher dimensions, lie close together, and their orientation can be ordered because they must fall on a path which is a closed loop for a full rotation (Ourmazd et al, 2010; Hosseinizadeh et al, 2014) This method has recently been used to obtain the first experimental conformational movie of an icosahedral virus and determination of its reaction coordinate during extrusion of a viral genome (Hosseinizadeh et al, 2017). There are successful cases demonstrating the application of these algorithms in handling heterogeneous sample data, where Kassemeyer et al (2013) used the geodesic and in-plane rotations algorithm (GIPRAL) to select the CDI data that correspond to the same sized particles Detailed discussions of these approaches were recently reviewed (Liu & Spence, 2016). In the related field of single-particle cryo-EM, where real-space images solve the phase problem and the Friedel symmetry is not imposed, the maximum likelihood method with Bayesian statistics (Scheres, 2012) has been used to iteratively classify images with different conformations by sorting them according to both orientation and a limited number of conformational classes

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Discussion

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