An advanced workflow for single particle imaging with the limited data at an X-ray free-electron laser

TL;DR

This paper presents an improved workflow for single particle imaging with limited data at an X-ray free-electron laser, enabling 3D structure determination of bacteriophage PR772 at 6.9 nm resolution.

Contribution

It introduces modifications to existing SPI analysis methods, including EM-based classification and mode decomposition, to handle data limitations and improve structure determination.

Findings

Achieved 6.9 nm resolution of bacteriophage PR772 structure

Enhanced analysis pipeline handles limited data and detector issues

Demonstrated structure determination without symmetry constraints

Abstract

An improved analysis for single particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the AMO instrument at the Linac Coherent Light Source (LCLS) as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from the half of the detector and small fraction of single hits. General SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus structure determination step. The presented processing pipeline allowed us to determine the three-dimensional structure of the bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.