An iterative refinement method combining detector geometry optimization and diffraction model refinement in serial femtosecond crystallography

Background Recent advances in serial femtosecond crystallography(SFX)using X-ray free electron lasers(XFELs)have facilitated accurate structure determination for biological macromolecules.However,given the many fluctuations inherent in SFX,the acquisition of SFX data of sufficiently high quality still remains challenging.Method Aimed at enhancing the accuracy of SFX data,this study proposes an iterative refinement method to optimally match pairs of the observed and predicted reflections on the detector plane.This method features a combination of detector geometry optimization and diffraction model refinement in an alternate manner,concomitant with a cycle-by-cycle peak selection procedure.Result To demonstrate whether this iterative method is convergent and feasible,both numerical simulations and experimental tests have been performed.The results reveal that this method can gradually improve overall quality of the integrated SFX data and therefore accelerate the convergence of Monte Carlo integration,while simultaneously suppressing correlations inherent in certain parameters and precluding outliers to some extent during the refinement.Conclusion We have demonstrated that our iterative refinement method is applicable to both simulated and experimental SFX data.It is expected that this method could provide meaningful insights into the refinement of SFX data and take the step forward toward more accurate Monte Carlo integration.

XFEL data analysis for structural biology

X-ray Free Electron Lasers （XFELs） have advanced research in structure biology, by exploiting their ultra-short and bright X-ray pulses. The resulting ＂diffraction before destruction＂ experimental approach allows data collection to outrun radiation damage, a crucial factor that has often limited resolution in the structure determination of biological molecules. Since the first hard X-ray laser （the Linac Coherent Light Source （LCLS） at SLAC） commenced operation in 2009, serial femtosecond crystallography （SFX） has rapidly matured into a method for the structural analysis of nano- and micro-crystals. At the same time, single particle structure determination by coherent diffractive imaging, with one particle （such as a virus） per shot, has been under intense development. In this review we describe these applications of X-ray lasers in structural biology, with a focus particularly on aspects of data analysis for the computational research community. We summarize the key problems in data analysis and model reconstruction, and provide perspectives on future research using computational methods.

Fluid sample injectors for x-ray free electron laser at SACLA

This paper provides a review on sample injectors which are provided at SPring-8 Angstrom Compact free electron LAser(SACLA) for conducting serial measurement in a ‘diffract-before-destroy' scheme using an x-ray free electron laser(XFEL). Versatile experimental platforms at SACLA are able to accept various types of injectors, among which liquidjet, droplet and viscous carrier injectors are frequently utilized. These injectors produce different forms of fluid targets such as a liquid filament with a diameter in the order of micrometer, micro-droplet synchronized to XFEL pulses, and slowly flowing column of highly viscous fluid with a rate below 1 μL min-1. Characteristics and applications of the injectors are described.