Multiple-beamline operation of SACLA

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds

There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.

Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction

Single-particle analysis using x-ray free-electron lasers (XFELs) is a novel method for obtaining structural information of samples in a state close to nature. In particular, it is suitable for observing the inner structure of large biomolecules by taking advantage of the high transmittance of x-rays. However, systematic studies on the resolution achievable for large molecules are lacking. In this study, the molecular size dependence of the resolution of a three-dimensional (3D) structure resulting from XFEL single-particle reconstruction is evaluated using synthetic data. Evidently, 3D structures of larger molecules can be restored with higher detail (defined relative to the molecular sizes) than smaller ones; however, reconstruction with high absolute resolution (defined in nm^-1) is challenging. Our results provide useful information for the experimental design of 3D structure reconstruction using coherent x-ray diffraction patterns of single-particles.

High-fluence and high-gain multilayer focusing optics to enhance spatial resolution in femtosecond X-ray laser imaging

With the emergence of X-ray free-electron lasers (XFELs), coherent diffractive imaging (CDI) has acquired a capability for single-particle imaging (SPI) of non-crystalline objects under non-cryogenic conditions. However, the single-shot spatial resolution is limited to ~5 nanometres primarily because of insufficient fluence. Here, we present a CDI technique whereby high resolution is achieved with very-high-fluence X-ray focusing using multilayer mirrors with nanometre precision. The optics can focus 4-keV XFEL down to 60 nm × 110 nm and realize a fluence of >3 × 10⁵ J cm⁻² pulse⁻¹ or >4 × 10¹² photons μm⁻² pulse⁻¹ with a tenfold increase in the total gain compared to conventional optics due to the high demagnification. Further, the imaging of fixed-target metallic nanoparticles in solution attained an unprecedented 2-nm resolution in single-XFEL-pulse exposure. These findings can further expand the capabilities of SPI to explore the relationships between dynamic structures and functions of native biomolecular complexes.

Here, the authors realize an ultra-high fluence X-ray laser by high-gain multilayer focusing optics. This enables in-solution imaging with 2-nm resolution in a single-pulse exposure, making strides toward biomolecular imaging under physiological conditions.

Features and futures of X-ray free-electron lasers

Linear accelerator-based free-electron lasers (FELs) are the leading source of fully coherent X-rays with ultra-high peak powers and ultra-short pulse lengths. Current X-ray FEL facilities have proved their worth as useful tools for diverse scientific applications. In this paper, we present an overview of the features and future prospects of X-ray FELs, including the working principles and properties of X-ray FELs, the operational status of different FEL facilities worldwide, the applications supported by such facilities, and the current developments and outlook for X-ray FEL-based research.

Synchrotron Radiation in Periodic Magnetic Fields of FEL Undulators—Theoretical Analysis for Experiments

A theoretical study of the synchrotron radiation (SR) from electrons in periodic magnetic fields with non-periodic magnetic components is presented. It is applied to several free electron lasers (FELs) accounting for the real characteristics of their electron beams: finite sizes, energy spread, divergence etc. All the losses and off-axis effects are accounted analytically. Exact expressions for the harmonic radiation in multiperiodic magnetic fields with non-periodic components and off-axis effects are given in terms of the generalized Bessel and Airy-type functions. Their analytical forms clearly distinguish all contributions in each polarization of the undulator radiation (UR). The application to FELs is demonstrated with the help of the analytical model for FEL harmonic power evolution, which accounts for all major losses and has been verified with the results of well documented FEL experiments. The analysis of the off-axis effects for the odd and even harmonics is performed for SPRING8 Angstrom Compact free-electron LAser (SACLA) and Pohang Accelerator Laboratory (PAL-XFEL). The modelling describes theoretically the power levels of odd and even harmonics and the spectral line width and shape. The obtained theoretical results agree well with the available data for FEL experiments; where no data exist, we predict and explain the FEL radiation properties. The proposed theoretical approach is applicable to practically any FEL.

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

Viscosity-adjustable grease matrices for serial nanocrystallography

Serial femtosecond crystallography (SFX) has enabled determination of room temperature structures of proteins with minimum radiation damage. A highly viscous grease matrix acting as a crystal carrier for serial sample loading at a low flow rate of ~0.5 μl min⁻¹ was introduced into the beam path of X-ray free-electron laser. This matrix makes it possible to determine the protein structure with a sample consumption of less than 1 mg of the protein. The viscosity of the matrix is an important factor in maintaining a continuous and stable sample column from a nozzle of a high viscosity micro-extrusion injector for serial sample loading. Using conventional commercial grease (an oil-based, viscous agent) with insufficient control of viscosity in a matrix often gives an unexpectedly low viscosity, providing an unstable sample stream, with effects such as curling of the stream. Adjustment of the grease viscosity is extremely difficult since the commercial grease contains unknown compounds, which may act as unexpected inhibitors of proteins. This study introduces two novel grease matrix carriers comprising known compounds with a viscosity higher than that of conventional greases, to determine the proteinase K structure from nano-/microcrystals.

High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures

Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca (SaBphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.

An experimental platform using high-power, high-intensity optical lasers with the hard X-ray free-electron laser at SACLA

An experimental platform using X-ray free-electron laser (XFEL) pulses with high-intensity optical laser pulses is open for early users' experiments at the SACLA XFEL facility after completion of the commissioning. The combination of the hard XFEL and the high-intensity laser provides capabilities to open new frontiers of laser-based high-energy-density science. During the commissioning phase, characterization of the XFEL and the laser at the platform has been carried out for the combinative utilization as well as the development of instruments and basic diagnostics for user experiments. An overview of the commissioning and the current capabilities of the experimental platform is presented.