With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its “off-time” between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.

We present a supervised deep neural network model for phase retrieval of coherent X-ray imaging and evaluate the performance. A supervised deep-learning-based approach requires a large amount of pre-training datasets. In most proposed models, the various experimental uncertainties are not considered when the input dataset, corresponding to the diffraction image in reciprocal space, is generated. We explore the performance of the deep neural network model, which is trained with an ideal quality of dataset, when it faces real-like corrupted diffraction images. We focus on three aspects of data qualities such as a detection dynamic range, a degree of coherence and noise level. The investigation shows that the deep neural network model is robust to a limited dynamic range and partially coherent X-ray illumination in comparison to the traditional phase retrieval, although it is more sensitive to the noise than the iteration-based method. This study suggests a baseline capability of the supervised deep neural network model for coherent X-ray imaging in preparation for the deployment to the laboratory where diffraction images are acquired.

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.

We present a deep learning-based generative model for the enhancement of partially coherent diffractive images. In lensless coherent diffractive imaging, a highly coherent X-ray illumination is required to image an object at high resolution. Non-ideal experimental conditions result in a partially coherent X-ray illumination, lead to imperfections of coherent diffractive images recorded on a detector, and ultimately limit the capability of lensless coherent diffractive imaging. The previous approaches, relying on the coherence property of illumination, require preliminary experiments or expensive computations. In this article, we propose a generative adversarial network (GAN) model to enhance the visibility of fringes in partially coherent diffractive images. Unlike previous approaches, the model is trained to restore the latent sharp features from blurred input images without finding coherence properties of illumination. We demonstrate that the GAN model performs well with both coherent diffractive imaging and ptychography. It can be applied to a wide range of imaging techniques relying on phase retrieval of coherent diffraction patterns.

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

Formamide, a simple model bio-molecule (HCONH2), is irradiated with high intensity, ultrashort pulses from an x-ray free electron laser. Ionic fragments resulting from photoionization and subsequent decay processes are recorded, as well as the electronic signature of the different inner shell ionization events that can take place during the x-ray pulses. The formation of double-core-hole states, where a second inner shell electron is removed before the first core hole has been refilled is observed in the electron spectra, recorded at all three sites (C, N, O) of the molecule. The individual ionization potentials are compared with results of ab initio calculations at different level of theory. Based on our results, future opportunities for advanced studies of inner-shell-induced electronic and nuclear dynamics are explored.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The ever-increasing brightness of synchrotron radiation sources demands improved x-ray optics to utilise their capability for imaging and probing biological cells, nano-devices, and functional matter on the nanometre scale with chemical sensitivity. Hard x-rays are ideal for high-resolution imaging and spectroscopic applications due to their short wavelength, high penetrating power, and chemical sensitivity. The penetrating power that makes x-rays useful for imaging also makes focusing them technologically challenging. Recent developments in layer deposition techniques that have enabled the fabrication of a series of highly focusing x-ray lenses, known as wedged multi layer Laue lenses. Improvements to the lens design and fabrication technique demands an accurate, robust, in-situ and at-wavelength characterisation method. To this end, we have developed a modified form of the speckle-tracking wavefront metrology method, the ptychographic x-ray speckle tracking method, which is capable of operating with highly divergent wavefields. A useful by-product of this method, is that it also provides high-resolution and aberration-free projection images of extended specimens. We report on three separate experiments using this method, where we have resolved ray path angles to within 4 nano-radians with an imaging resolution of 45nm (full-period). This method does not require a high degree of coherence, making it suitable for lab based x-ray sources. Likewise it is robust to errors in the registered sample positions making it suitable for x-ray free-electron laser facilities, where beam pointing fluctuations can be problematic for wavefront metrology.

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL will soon provide 27,000 pulses per second, more than two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Solids irradiated by energetic photons can be eroded in two modes, depending on the radiation intensity. High average, low-peak power sources, e.g., synchrotron radiation and high-order harmonics, induce desorption of the material at a low etch rate. In contrast, high-peak-power radiation from extreme ultraviolet and x-ray lasers usually causes a massive removal of the material even by a single shot. In this contribution, an effective material erosion is reported in PMMA exposed to multiple accumulated pulses generated by the free-electron x-ray-laser Linac Coherent Light Source (LCLS, tuned at a photon energy of 830 eV in this study, operated in Menlo Park at Stanford, CA, USA) at a fluence below the single-pulse ablation threshold. The effect is caused by polymer-chain scissions initiated by single photons carrying enough energy to break the C-C bounds. High efficiency of the erosion is supposed to occur due to a correlation of the single-photon effects. The subthreshold damage exhibits a nonlinear dose dependence resulting from a competition between chain scissions and cross-linking processes. The cross-linking is proven by Raman spectroscopy of the irradiated polymer. Two theoretical models of the x-ray free-electron-laser-induced erosion are suggested, which provide an excellent agreement with the experimental results.

We provide a detailed description of a serial femtosecond crystallography (SFX) dataset collected at the European X-ray free-electron laser facility (EuXFEL). The EuXFEL is the first high repetition rate XFEL delivering MHz X-ray pulse trains at 10 Hz. The short spacing (<1 µs) between pulses requires fast flowing microjets for sample injection and high frame rate detectors. A data set was recorded of a microcrystalline mixture of at least three different jack bean proteins (urease, concanavalin A, concanavalin B). A one megapixel Adaptive Gain Integrating Pixel Detector (AGIPD) was used which has not only a high frame rate but also a large dynamic range. This dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development and for data analysis training for prospective XFEL users.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

The free-electron laser FLASH2, a variable gap undulators line, has opened new scientific possibilities for users at DESY in the Hamburg area [1]. The current pulsed radiation at the FLASH facility primarily relies on the SASE process. Thus, the beam characteristics may differ drastically from pulse to pulse; requiring single-shot photon diagnostics and characterization of the photon beam parameters. The beamline FL24 at FLASH2 is equipped with a set of bendable Kirkpatrick-Baez (KB) mirrors which can strongly focus the beam down to a few micrometers. As a key parameter for many experiments, understanding of the focus characteristics and variations is demanded by users. The current instrumentation at the beamline FL24 has foreseen a dedicated Hartmann-Wavefront Sensor (HWS) to run the online, highly focused, single-shot beam characterization within the operating wavelength range of the FLASH2 [2]. However, a critical issue linked to the success of the current HWS is the assumption of high transverse coherence of the radiation. We observed a slight difference between the retrieved focuses by the HWS and those measured with the imprints method. We attribute the observed difference to the low-degree of the transverse coherence. Recently, we performed a non-destructive Young’s double-pinhole experiment, at the beamline FL24, which proved the variation of the degree of transverse coherence (25-50% deviation from the full coherence) correlated to the various machine parameters [3]. Advances in the Fresnel Diffractive Imaging (FDI) have promoted the FEL pulse characterization by reconstructing partially coherent wave fields. This approach was successfully applied to characterize highly transverse coherent, focused pulses at the beamline BL2 at the FLASH1 line [4]. We have extended the application of the FDI method, at the beamline FL24, to characterize the transverse partially coherent pulses, in a single-shot basis, and estimate a measure of the degree of the transverse coherence. Summarily, we report on the results of our previous pulse and transverse coherence characterization experiments, and discuss the feasibility of each method as an on-line photon diagnostic. Furthermore, our future plan to apply the partially coherent ptychography method [5] for the wave field characterization will be discussed providing the results of start-to-end simulations.---------------------------------------- References and links: 1. B. Faatz, et al. “The FLASH Facility: Advanced Options for FLASH2 and Future Perspectives," Applied Science 7, (2017). 2. B. Keitel, et al. “Hartmann wavefront sensors and their application at FLASH," Special Issue (PhotonDiag2015), J. Synchrotron Rad. 23, (2016). 3. T. Wodzinski, et al. “Coherence measurements with double pinholes at FLASH2," PhotonDiag 2018, Hamburg, Germany. 4. M. Mehrjoo, et al, “Single-Shot Determination of Focused FEL Wave Fields using Iterative Phase Retrieval," Opt. Express,25, (2017). 5. N. Burdet. et al, “Evaluation of partial coherence correction in X-ray ptychography ," Opt. Express, 5, (2015).

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.