Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data.

Toshiyuki Nishiyama,Kiyoshi Ueda,Yasumasa Joti,Yuta Ito,Christoph Bostedt,Takaki Hatsui,Christophe Nicolas,Catalin Miron,Kensuke Tono,Makina Yabashi,Takashi Kameshima,Takayuki Umemoto,Subhendu Mondal,Tsukasa Sakai,Kazuhiro Matsuda,Akinobu Niozu,H Fukuzawa ,Ken Ferguson ,K Matsunami ,Yoshibumi Sato ,S Wada ,C Hutchison ,K Nagaya ,Takehiko Tachibana ,K Motomura ,Wenzhen Xu

doi:10.1107/s2052252519014222

Abstract

With the emergence of X-ray free-electron lasers, it is possible to investigate the structure of nanoscale samples by employing coherent diffractive imaging in the X-ray spectral regime. In this work, we developed a refinement method for structure reconstruction applicable to low-quality coherent diffraction data. The method is based on the gradient search method and considers the missing region of a diffraction pattern and the small number of detected photons. We introduced an initial estimate of the structure in the method to improve the convergence. The present method is applied to an experimental diffraction pattern of an Xe cluster obtained in an X-ray scattering experiment at the SPring-8 Angstrom Compact free-electron LAser (SACLA) facility. It is found that the electron density is successfully reconstructed from the diffraction pattern with a large missing region, with a good initial estimate of the structure. The diffraction pattern calculated from the reconstructed electron density reproduced the observed diffraction pattern well, including the characteristic intensity modulation in each ring. Our refinement method enables structure reconstruction from diffraction patterns under difficulties such as missing areas and low diffraction intensity, and it is potentially applicable to the structure determination of samples that have low scattering power.

Highlights

The recent advent of X-ray free-electron lasers (XFELs) has offered new opportunities to investigate the structure of a single nanoscale sample by using a shot-by-shot X-ray diffraction method on the basis of the diffraction-beforedestruction scheme (Neutze et al, 2000)
A structure similar to this one has been reported in earlier studies involving X-ray scattering experiments using soft XFELs (Rupp et al, 2012, 2014), we succeeded in determining the size and shape of the nonspherical cluster using hard XFEL pulses
We developed a refinement method for structure reconstruction that combines the optimization algorithm based on the

Summary

Introduction

The recent advent of X-ray free-electron lasers (XFELs) has offered new opportunities to investigate the structure of a single nanoscale sample by using a shot-by-shot X-ray diffraction method on the basis of the diffraction-beforedestruction scheme (Neutze et al, 2000). Several studies (Takahashi et al, 2013; Kimura et al, 2014; van der Schot et al, 2015; Tanyag et al, 2015) have employed iterative PR algorithms to coherent diffraction patterns and demonstrated the feasibility of structure reconstruction of single particles. Unconstrained modes, which are not restricted by the available information in the real and Fourier space These modes give rise to the ambiguity of reconstruction and some studies show that removal of this ambiguity leads to a better convergence to structural reconstruction using PR (Thibault et al, 2006; Seibert et al, 2011). Another problem is the limited number of diffracted photons from single particles. We apply the method to a diffraction pattern from a giant Xe cluster recorded at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA) facility (Ishikawa et al, 2012)

Experiment

Refinement method

Results and discussion

Conclusion

Funding information