A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus

The marine cyanobacterium Prochlorococcus is a main contributor to global photosynthesis, whilst being limited by iron availability. Cyanobacterial genomes generally encode two different types of FutA iron-binding proteins: periplasmic FutA2 ABC transporter subunits bind Fe(III), while cytosolic FutA1 binds Fe(II). Owing to their small size and their economized genome Prochlorococcus ecotypes typically possess a single futA gene. How the encoded FutA protein might bind different Fe oxidation states was previously unknown. Here, we use structural biology techniques at room temperature to probe the dynamic behavior of FutA. Neutron diffraction confirmed four negatively charged tyrosinates, that together with a neutral water molecule coordinate iron in trigonal bipyramidal geometry. Positioning of the positively charged Arg103 side chain in the second coordination shell yields an overall charge-neutral Fe(III) binding state in structures determined by neutron diffraction and serial femtosecond crystallography. Conventional rotation X-ray crystallography using a home source revealed X-ray-induced photoreduction of the iron center with observation of the Fe(II) binding state; here, an additional positioning of the Arg203 side chain in the second coordination shell maintained an overall charge neutral Fe(II) binding site. Dose series using serial synchrotron crystallography and an XFEL X-ray pump-probe approach capture the transition between Fe(III) and Fe(II) states, revealing how Arg203 operates as a switch to accommodate the different iron oxidation states. This switching ability of the Prochlorococcus FutA protein may reflect ecological adaptation by genome streamlining and loss of specialized FutA proteins.

The Influence of B4C Film Density on Damage Threshold Based on Monte Carlo Method for X-ray Mirror

The uniformity and consistency of X-ray mirror film materials prepared by experimental methods are difficult to guarantee completely. These factors directly affect the service life of free electron laser devices in addition to its own optical properties. Therefore, the quality of the film material, especially the density, has a critical effect on its application. Boron carbide film and monocrystalline silicon substrate were suitable examples to explore their influence of density on the damage threshold based on Monte Carlo and heat-conduction methods. Through simulation results, it was found that the change in film density could affect the energy deposition depth and damage threshold. When the film density was 2.48 g/cm3, it had relatively high damage threshold in all energy ranges. And then the specific incident parameter for practical application was investigated. It was found that the damage mechanism of the B4C/Si was the melting of the interface. And the damage threshold was also higher with the film density of 2.48 g/cm3. Therefore, it was recommended to maintain the density at this value as far as possible when preparing the film, and to ensure the uniformity and consistency of the film material.

X-ray free-electron laser induced acoustic microscopy (XFELAM)

The X-ray free-electron laser (XFEL) has remarkably advanced X-ray imaging technology and enabled important scientific achievements. The XFEL's extremely high power, short pulse width, low emittance, and high coherence make possible such diverse imaging techniques as absorption/emission spectroscopy, diffraction imaging, and scattering imaging. Here, we demonstrate a novel XFEL-based imaging modality that uses the X-ray induced acoustic (XA) effect, which we call X-ray free-electron laser induced acoustic microscopy (XFELAM). Initially, we verified the XA effect by detecting XA signals from various materials, then we validated the experimental results with simulation outcomes. Next, in resolution experiments, we successfully imaged a patterned tungsten target with drilled various-sized circles at a spatial resolution of 7.8 ± 5.1 µm, which is the first micron-scale resolution achieved by XA imaging. Our results suggest that the novel XFELAM can expand the usability of XFEL in various areas of fundamental scientific research.

Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated from natural crystals using MHz-SFX

The Lysinibacillus sphaericus proteins Tpp49Aa1 and Cry48Aa1 can together act as a toxin toward the mosquito Culex quinquefasciatus and have potential use in biocontrol. Given that proteins with sequence homology to the individual proteins can have activity alone against other insect species, the structure of Tpp49Aa1 was solved in order to understand this protein more fully and inform the design of improved biopesticides. Tpp49Aa1 is naturally expressed as a crystalline inclusion within the host bacterium, and MHz serial femtosecond crystallography using the novel nanofocus option at an X-ray free electron laser allowed rapid and high-quality data collection to determine the structure of Tpp49Aa1 at 1.62 Å resolution. This revealed the packing of Tpp49Aa1 within these natural nanocrystals as a homodimer with a large intermolecular interface. Complementary experiments conducted at varied pH also enabled investigation of the early structural events leading up to the dissolution of natural Tpp49Aa1 crystals-a crucial step in its mechanism of action. To better understand the cooperation between the two proteins, assays were performed on a range of different mosquito cell lines using both individual proteins and mixtures of the two. Finally, bioassays demonstrated Tpp49Aa1/Cry48Aa1 susceptibility of Anopheles stephensi, Aedes albopictus, and Culex tarsalis larvae-substantially increasing the potential use of this binary toxin in mosquito control.

Tracking the structural dynamics of proteins with time-resolved X-ray solution scattering

Relevant events during protein function such as ligand binding/release and interaction with substrates or with light are often accompanied by out-of-equilibrium structural dynamics. Time-resolved experimental techniques have been developed to follow protein structural changes as they happen in real time after a given reaction-triggering event. Time-resolved X-ray solution scattering is a promising approach that bears structural sensitivity with temporal resolution in the femto-to-millisecond time range, depending on the X-ray source characteristics and the triggering method. Here we present the basic principles of the technique together with a description of the most relevant results recently published and a discussion on the computational methods currently developed to achieve a structural interpretation of the time-resolved X-ray solution scattering experimental data.

Stability of Bragg reflectors under megahertz heat load at XFELs

Modern X-ray free-electron laser (XFEL) sources can deliver photon pulses with millijoule pulse energies and megahertz repetition rate. As shown by the simulations in this work, for particular cases the dynamical heat load effects for Bragg reflectors could cause problems at these facilities. These problems would be underestimated if only quasi-static thermoelastic simulations are considered. Nevertheless, for the sake of simplicity the quasi-static approach is a common choice for estimating heat load effects. To emphasize the relevance of dynamical thermoelastic effects, the response to the partial absorption of an X-ray pulse, as provided by a saturated X-ray free-electron laser oscillator (XFELO) in a single crystal diamond with a thickness of 100 µm and lateral dimensions in the millimetre range, is discussed in this work. The outcome of the dynamic thermoelastic simulations indicates a clear dominance regarding the strain value reached, which is present for consecutive X-ray matter interactions with megahertz repetition rate.

Towards pump-probe single-crystal XFEL refinements for small-unit-cell systems

Serial femtosecond crystallography for small-unit-cell systems has so far seen very limited application despite obvious scientific possibilities. This is because reliable data reduction has not been available for these challenging systems. In particular, important intensity corrections such as the partiality correction critically rely on accurate determination of the crystal orientation, which is complicated by the low number of diffraction spots for small-unit-cell crystals. A data reduction pipeline capable of fully automated handling of all steps of data reduction from spot harvesting to merged structure factors has been developed. The pipeline utilizes sparse indexing based on known unit-cell parameters, seed-skewness integration, intensity corrections including an overlap-based combined Ewald sphere width and partiality correction, and a dynamically adjusted post-refinement routine. Using the pipeline, data measured on the compound K₄[Pt₂(P₂O₅H₂)₄]·2H₂O have been successfully reduced and used to solve the structure to an R₁ factor of ∼9.1%. It is expected that the pipeline will open up the field of small-unit-cell serial femtosecond crystallography experiments and allow investigations into, for example, excited states and reaction intermediate chemistry.

Megahertz-rate ultrafast X-ray scattering and holographic imaging at the European XFEL

The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, results from the first megahertz-repetition-rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL are presented. The experimental capabilities that the SCS instrument offers, resulting from the operation at megahertz repetition rates and the availability of the novel DSSC 2D imaging detector, are illustrated. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative, providing an ideal test-bed for operation at megahertz rates. Our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.

Towards performing high-resolution inelastic X-ray scattering measurements at hard X-ray free-electron lasers coupled with energetic laser drivers

High-resolution inelastic X-ray scattering is an established technique in the synchrotron community, used to investigate collective low-frequency responses of materials. When fielded at hard X-ray free-electron lasers (XFELs) and combined with high-intensity laser drivers, it becomes a promising technique for investigating matter at high temperatures and high pressures. This technique gives access to important thermodynamic properties of matter at extreme conditions, such as temperature, material sound speed, and viscosity. The successful realization of this method requires the acquisition of many identical laser-pump/X-ray-probe shots, allowing the collection of a sufficient number of photons necessary to perform quantitative analyses. Here, a 2.5-fold improvement in the energy resolution of the instrument relative to previous works at the Matter in Extreme Conditions (MEC) endstation, Linac Coherent Light Source (LCLS), and the High Energy Density (HED) instrument, European XFEL, is presented. Some aspects of the experimental design that are essential for improving the number of photons detected in each X-ray shot, making such measurements feasible, are discussed. A careful choice of the energy resolution, the X-ray beam mode provided by the XFEL, and the position of the analysers used in such experiments can provide a more than ten-fold improvement in the photometrics. The discussion is supported by experimental data on 10 µm-thick iron and 50 nm-thick gold samples collected at the MEC endstation at the LCLS, and by complementary ray-tracing simulations coupled with thermal diffuse scattering calculations.

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

[This corrects the article DOI: 10.1107/S2052252520012798.].

Crystallographic Studies of Rhodopsins: Structure and Dynamics

Crystal structures have provided detailed insight in the architecture of rhodopsin photoreceptors. Of particular interest are the protein-chromophore interactions that govern the light-induced retinal isomerization and ultimately induce the large structural changes important for the various biological functions of the family. The reaction intermediates occurring along the rhodopsin photocycle have vastly differing lifetimes, from hundreds of femtoseconds to milliseconds. Detailed insight at high spatial and temporal resolution can be obtained by time-resolved crystallography using pump-probe approaches at X-ray free-electron lasers. Alternatively, cryotrapping approaches can be used. Both the approaches are described, including illumination and sample delivery. The importance of appropriate photoexcitation avoiding multiphoton absorption is stressed.

Crystallization kinetics of atomic crystals revealed by a single-shot and single-particle X-ray diffraction experiment

Crystallization is a fundamental natural phenomenon and the ubiquitous physical process in materials science for the design of new materials. So far, experimental observations of the structural dynamics in crystallization have been mostly restricted to slow dynamics. We present here an exclusive way to explore the dynamics of crystallization in highly controlled conditions (i.e., in the absence of impurities acting as seeds of the crystallites) as it occurs in vacuum. We have measured the early formation stage of solid Xe nanoparticles nucleated in an expanding supercooled Xe jet by means of an X-ray diffraction experiment with 10-fs X-ray free-electron laser (XFEL) pulses. We found that the structure of Xe nanoparticles is not pure face-centered cubic (fcc), the expected stable phase, but a mixture of fcc and randomly stacked hexagonal close-packed (rhcp) structures. Furthermore, we identified the instantaneous coexistence of the comparably sized fcc and rhcp domains in single Xe nanoparticles. The observations are explained by the scenario of structural aging, in which the nanoparticles initially crystallize in the highly stacking-disordered rhcp phase and the structure later forms the stable fcc phase. The results are reminiscent of analogous observations in hard-sphere systems, indicating the universal role of the stacking-disordered phase in nucleation.

On incoherent diffractive imaging

Incoherent diffractive imaging (IDI) promises structural analysis with atomic resolution based on intensity interferometry of pulsed X-ray fluorescence emission. However, its experimental realization is still pending and a comprehensive theory of contrast formation has not been established to date. Explicit expressions are derived for the equal-pulse two-point intensity correlations, as the principal measured quantity of IDI, with full control of the prefactors, based on a simple model of stochastic fluorescence emission. The model considers the photon detection statistics, the finite temporal coherence of the individual emissions, as well as the geometry of the scattering volume. The implications are interpreted in view of the most relevant quantities, including the fluorescence lifetime, the excitation pulse, as well as the extent of the scattering volume and pixel size. Importantly, the spatiotemporal overlap between any two emissions in the sample can be identified as a crucial factor limiting the contrast and its dependency on the sample size can be derived. The paper gives rigorous estimates for the optimum sample size, the maximum photon yield and the expected signal-to-noise ratio under optimal conditions. Based on these estimates, the feasibility of IDI experiments for plausible experimental parameters is discussed. It is shown in particular that the mean number of photons per detector pixel which can be achieved with X-ray fluorescence is severely limited and as a consequence imposes restrictive constraints on possible applications.

Biophysical applications in structural and molecular biology

The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn't be solved by X-ray crystallography or NMR. Now a day's low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.

The photon beamline vacuum system of the European XFEL

The photon beamline vacuum system of the European X-ray Free-Electron Laser Facility (European XFEL) is described. The ultra-large, in total more than 3 km-long, fan-like vacuum system, consisting of three photon beamlines is an essential part of the photon beam transport. It is located between the accelerator vacuum system and the scientific instruments. The main focus of the design was on the efficiency, reliability and robustness of the entire system to ensure the retention of beam properties and the operation of the X-ray optics and X-ray photon diagnostics components. Installation started in late 2014, the first of the three beamline vacuum systems was commissioned in spring 2017, and the last one was operational in mid-2018. The present state and experience from the first years of operation are outlined.

Recent Advances and Future Perspectives on Microfluidic Mix-and-Jet Sample Delivery Devices

The integration of the Gas Dynamic Virtual Nozzle (GDVN) and microfluidic technologies has proven to be a promising sample delivery solution for biomolecular imaging studies and has the potential to be transformative for a range of applications in physics, biology, and chemistry. Here, we review the recent advances in the emerging field of microfluidic mix-and-jet sample delivery devices for the study of biomolecular reaction dynamics. First, we introduce the key parameters and dimensionless numbers involved in their design and characterisation. Then we critically review the techniques used to fabricate these integrated devices and discuss their advantages and disadvantages. We then summarise the most common experimental methods used for the characterisation of both the mixing and jetting components. Finally, we discuss future perspectives on the emerging field of microfluidic mix-and-jet sample delivery devices. In summary, this review aims to introduce this exciting new topic to the wider microfluidics community and to help guide future research in the field.

Materials Imaging and Dynamics (MID) instrument at the European X-ray Free-Electron Laser Facility

The Materials Imaging and Dynamics (MID) instrument at the European X-ray Free-Electron Laser (EuXFEL) facility is described. EuXFEL is the first hard X-ray free-electron laser operating in the MHz repetition range which provides novel science opportunities. The aim of MID is to enable studies of nano-structured materials, liquids, and soft- and hard-condensed matter using the bright X-ray beams generated by EuXFEL. Particular emphasis is on studies of structure and dynamics in materials by coherent scattering and imaging using hard X-rays. Commission of MID started at the end of 2018 and first experiments were performed in 2019.

A high-power, high-repetition-rate THz source for pump-probe experiments at Linac Coherent Light Source II

Experiments using a THz pump and an X-ray probe at an X-ray free-electron laser (XFEL) facility like the Linac Coherent Light Source II (LCLS II) require frequency-tunable (3 to 20 THz), narrow bandwidth (∼10%), carrier-envelope-phase-stable THz pulses that produce high fields (>1 MV cm^-1) at the repetition rate of the X-rays and are well synchronized with them. In this paper, a two-bunch scheme to generate THz radiation at LCLS II is studied: the first bunch produces THz radiation in an electromagnet wiggler immediately following the LCLS II undulator that produces X-rays from the second bunch. The initial time delay between the two bunches is optimized to compensate for the path difference in THz transport. The two-bunch beam dynamics, the THz wiggler and radiation are described, as well as the transport system bringing the THz pulses from the wiggler to the experimental hall.

The ePix10k 2-megapixel hard X-ray detector at LCLS

The ePix10ka2M (ePix10k) is a new large area detector specifically developed for X-ray free-electron laser (XFEL) applications. The hybrid pixel detector was developed at SLAC to provide a hard X-ray area detector with a high dynamic range, running at the 120 Hz repetition rate of the Linac Coherent Light Source (LCLS). The ePix10k consists of 16 modules, each with 352 × 384 pixels of 100 µm × 100 µm distributed on four ASICs, resulting in a 2.16 megapixel detector, with a 16.5 cm × 16.5 cm active area and ∼80% coverage. The high dynamic range is achieved with three distinct gain settings (low, medium, high) as well as two auto-ranging modes (high-to-low and medium-to-low). Here the three fixed gain modes are evaluated. The resulting dynamic range (from single photon counting to 10000 photons pixel-1 pulse-1 at 8 keV) makes it suitable for a large number of different XFEL experiments. The ePix10k replaces the large CSPAD in operation since 2011. The dimensions of the two detectors are similar, making the upgrade from CSPAD to ePix10k straightforward for most setups, with the ePix10k improving on experimental performance. The SLAC-developed ePix cameras all utilize a similar platform, are tailored to target different experimental conditions and are designed to provide an upgrade path for future high-repetition-rate XFELs. Here the first measurements on this new ePix10k detector are presented and the performance under typical XFEL conditions evaluated during an LCLS X-ray diffuse scattering experiment measuring the 9.5 keV X-ray photons scattered from a thin liquid jet.

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 × 10-4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10-3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

Cinema:Bandit: a visualization application for beamline science demonstrated on XFEL shock physics experiments

A new visualization tool, Cinema:Bandit, and its demonstration with a continuous workflow for analyzing shock physics experiments and visually exploring the data in real time at X-ray light sources is presented. Cinema:Bandit is an open-source, web-based visualization application in which the experimenter may explore an aggregated dataset to inform real-time beamline decisions and enable post hoc data analysis. The tool integrates with experimental workflows that process raw detector data into a simple database format, and it allows visualization of disparate data types, including experimental parameters, line graphs, and images. Use of parallel coordinates accommodates the irregular sampling of experimental parameters and allows for display and filtering of both experimental inputs and measurements. The tool is demonstrated on a dataset of shock-compressed titanium collected at the Matter in Extreme Conditions hutch at the Linac Coherent Light Source.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.

Transmission measurement at the Bernina branch of the Aramis Beamline of SwissFEL

The transmission of the optical components of the Bernina branch of the Aramis beamline at SwissFEL has been measured with an X-ray gas monitor from DESY and compared with a PSI gas detector upstream of the optical components. The transmission efficiencies of the Mo, Si and SiC mirror coatings of the Aramis beamline and the various other in-beam components were evaluated and compared with theoretical calculations, showing an agreement of 6% or better in all cases. The experiment has also shown the efficacy of the high-harmonic rejection mirrors at the Bernina branch of the Aramis beamline at SwissFEL, and characterized the transmission efficiency of the on-line spectrometer in the Aramis beamline. The theoretical transmission of the mirror coatings match the experimental data to within 7%. The accuracy of these measurements was checked against a radiative bolometer from a Japanese collaboration and found to agree to a level of 4% or better. Further comparisons with a diamond detector from a US-based inter-institute collaboration demonstrated a good agreement for the attenuator settings of the beamline.

Polyhedra, spindles, phage nucleus and pyramids: Structural biology of viral superstructures

Viral infection causes comprehensive rearrangements of the cell that reflect as much host defense mechanisms as virus-induced structures assembled to facilitate infection. Regardless of their pro- or antiviral role, large intracellular structures are readily detectable by microscopy and often provide a signature characteristic of a specific viral infection. The structural features and localization of these assemblies have thus been commonly used for the diagnostic and classification of viruses since the early days of virology. More recently, characterization of viral superstructures using molecular and structural approaches have revealed very diverse organizations and roles, ranging from dynamic viral factories behaving like liquid organelles to ultra-stable crystals embedding and protecting virions. This chapter reviews the structures, functions and biotechnological applications of virus-induced superstructures with a focus on assemblies that have a regular organization, for which detailed structural descriptions are available. Examples span viruses infecting all domains of life including the assembly of virions into crystalline arrays in eukaryotic and bacterial viruses, nucleus-like compartments involved in the replication of large bacteriophages, and pyramid-like structures mediating the egress of archaeal viruses. Among these superstructures, high-resolution structures are available for crystalline objects produced by insect viruses: viral polyhedra which function as the infectious form of occluded viruses, and spindles which are potent virulence factors of entomopoxviruses. In turn, some of these highly symmetrical objects have been used to develop and validate advanced structural approaches, pushing the boundary of structural biology.

xcalib: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms

The xcalib toolkit has been developed to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence-dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core-hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.

First measurements with the K-monochromator at the European XFEL

Hard X-ray free-electron lasers (XFELs) generate intense coherent X-ray beams by passing electrons through undulators, i.e. very long periodic magnet structures, which extend over hundreds of meters. The SASE1 and SASE2 undulator systems of the European XFEL consist of 35 segments with variable-gap planar undulators which are initially tuned to precise on-axis magnetic field strengths in a magnetic measurement laboratory to keep an important quality parameter - the K-value variation from segment to segment - below a certain limit (3 × 10^-4 for 12 keV photon energy). After tunnel installation only photon-based methods can determine the K-values of undulator segments with a similar accuracy. The synchrotron radiation from a single or a few segments can be spectrally filtered by a dedicated crystal monochromator (K-monochromator) and recorded with a photodiode or with an imager that provides 2D information, tuned for high sensitivity to detect low photon densities from distant single undulator segments. This instrumentation is applied for electron orbit analysis and optimization, and adjustment of individual undulators in terms of their central magnetic axis with respect to the electron beam. Single undulator segments were analysed by scanning the monochromator crystal angle and detecting the steepest slope of a photodiode signal. Alternatively, in the imaging method, an imager recorded the radiation cone of electrons passing through the undulator segment. From the spatial distribution of the radiation, the K-parameter was determined with a sufficiently high relative accuracy.

Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography

Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation

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.

On-line monitoring of the spatial properties of hard X-ray free-electron lasers based on a grating splitter

X-ray free-electron lasers (XFELs) play an increasingly important role in addressing the new scientific challenges relating to their high brightness, high coherence and femtosecond time structure. As a result of pulse-by-pulse fluctuations, the pulses of an XFEL beam may demonstrate subtle differences in intensity, energy spectrum, coherence, wavefront, etc., and thus on-line monitoring and diagnosis of a single pulse are required for many XFEL experiments. Here a new method is presented, based on a grating splitter and bending-crystal analyser, for single-pulse on-line monitoring of the spatial characteristics including the intensity profile, coherence and wavefront, which was suggested and applied experimentally to the temporal diagnosis of an XFEL single pulse. This simulation testifies that the intensity distribution, coherence and wavefront of the first-order diffracted beam of a grating preserve the properties of the incident beam, by using the coherent mode decomposition of the Gaussian-Schell model and Fourier optics. Indicatively, the first-order diffraction of appropriate gratings can be used as an alternative for on-line monitoring of the spatial properties of a single pulse without any characteristic deformation of the principal diffracted beam. However, an interesting simulation result suggests that the surface roughness of gratings will degrade the spatial characteristics in the case of a partially coherent incident beam. So, there exists a suitable roughness value for non-destructive monitoring of the spatial properties of the downstream beam, which depends on the specific optical path. Here, experiments based on synchrotron radiation X-rays are carried out in order to verify this method in principle. The experimental results are consistent with the theoretical calculations.

Biophysical Techniques in Structural Biology

Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.

Why conferences matter - musings from a crystallographic meeting

Despite extraordinary advances in the options available for instant electronic communication, the argument is made that conferences still provide a unique forum for transmission of new ideas and advances in science, with their ability to inspire attendees.

SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data

SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008 ▸), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012 ▸), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.

Crystallography on a chip - without the chip: sheet-on-sheet sandwich

Crystallography chips are fixed-target supports consisting of a film (for example Kapton) or wafer (for example silicon) that is processed using semiconductor-microfabrication techniques to yield an array of wells or through-holes in which single microcrystals can be lodged for raster-scan probing. Although relatively expensive to fabricate, chips offer an efficient means of high-throughput sample presentation for serial diffraction data collection at synchrotron or X-ray free-electron laser (XFEL) sources. Truly efficient loading of a chip (one microcrystal per well and no wastage during loading) is nonetheless challenging. The wells or holes must match the microcrystal size of interest, requiring that a large stock of chips be maintained. Raster scanning requires special mechanical drives to step the chip rapidly and with micrometre precision from well to well. Here, a `chip-less' adaptation is described that essentially eliminates the challenges of loading and precision scanning, albeit with increased, yet still relatively frugal, sample usage. The device consists simply of two sheets of Mylar with the crystal solution sandwiched between them. This sheet-on-sheet (SOS) sandwich structure has been employed for serial femtosecond crystallography data collection with micrometre-sized crystals at an XFEL. The approach is also well suited to time-resolved pump-probe experiments, in particular for long time delays. The SOS sandwich enables measurements under XFEL beam conditions that would damage conventional chips, as documented here. The SOS sheets hermetically seal the sample, avoiding desiccation of the sample provided that the X-ray beam does not puncture the sheets. This is the case with a synchrotron beam but not with an XFEL beam. In the latter case, desiccation, setting radially outwards from each punched hole, sets lower limits on the speed and line spacing of the raster scan. It is shown that these constraints are easily accommodated.

Improving signal strength in serial crystallography with DIALS geometry refinement

The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV-Vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolved X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. It is shown that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute, i.e. the change in Pt-Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, it is discussed how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the instrument response function.

Pulse-resolved intensity measurements at a hard X-ray FEL using semi-transparent diamond detectors

Solid-state ionization chambers are presented based on thin diamond crystals that allow pulse-resolved intensity measurements at a hard X-ray free-electron laser (FEL), up to the 4.5 MHz repetition rate that will become available at the European XFEL. Due to the small X-ray absorption of diamond the thin detectors are semi-transparent which eases their use as non-invasive monitoring devices in the beam. FELs are characterized by strong pulse-to-pulse intensity fluctuations due to the self-amplified spontaneous emission (SASE) process and in many experiments it is mandatory to monitor the intensity of each individual pulse. Two diamond detectors with different electrode materials, beryllium and graphite, were tested as intensity monitors at the XCS endstation of the Linac Coherent Light Source (LCLS) using the pink SASE beam at 9 keV. The performance is compared with LCLS standard monitors that detect X-rays backscattered from thin SiN foils placed in the beam. The graphite detector can also be used as a beam position monitor although with rather coarse resolution.

The slip-and-slide algorithm: a refinement protocol for detector geometry

Geometry correction is traditionally plagued by mis-fitting of correlated parameters, leading to local minima which prevent further improvements. Segmented detectors pose an enhanced risk of mis-fitting: even a minor confusion of detector distance and panel separation can prevent improvement in data quality. The slip-and-slide algorithm breaks down effects of the correlated parameters and their associated target functions in a fundamental shift in the approach to the problem. Parameters are never refined against the components of the data to which they are insensitive, providing a dramatic boost in the exploitation of information from a very small number of diffraction patterns. This algorithm can be applied to exploit the adherence of the spot-finding results prior to indexing to a given lattice using unit-cell dimensions as a restraint. Alternatively, it can be applied to the predicted spot locations and the observed reflection positions after indexing from a smaller number of images. Thus, the indexing rate can be boosted by 5.8% using geometry refinement from only 125 indexed patterns or 500 unindexed patterns. In one example of cypovirus type 17 polyhedrin diffraction at the Linac Coherent Light Source, this geometry refinement reveals a detector tilt of 0.3° (resulting in a maximal Z-axis error of ∼0.5 mm from an average detector distance of ∼90 mm) whilst treating all panels independently. Re-indexing and integrating with updated detector geometry reduces systematic errors providing a boost in anomalous signal of sulfur atoms by 20%. Due to the refinement of decoupled parameters, this geometry method also reaches convergence.

X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature

The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.

Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA

X-ray free-electron lasers (XFELs) have opened new opportunities for time-resolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TR-SFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inward_open state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inward_open state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.

Numerical simulations of the hard X-ray pulse intensity distribution at the Linac Coherent Light Source

Numerical simulations of the current and future pulse intensity distributions at selected locations along the Far Experimental Hall, the hard X-ray section of the Linac Coherent Light Source (LCLS), are provided. Estimates are given for the pulse fluence, energy and size in and out of focus, taking into account effects due to the experimentally measured divergence of the X-ray beam, and measured figure errors of all X-ray optics in the beam path. Out-of-focus results are validated by comparison with experimental data. Previous work is expanded on, providing quantitatively correct predictions of the pulse intensity distribution. Numerical estimates in focus are particularly important given that the latter cannot be measured with direct imaging techniques due to detector damage. Finally, novel numerical estimates of improvements to the pulse intensity distribution expected as part of the on-going upgrade of the LCLS X-ray transport system are provided. We suggest how the new generation of X-ray optics to be installed would outperform the old one, satisfying the tight requirements imposed by X-ray free-electron laser facilities.

Viscous hydrophilic injection matrices for serial crystallography

Serial (femtosecond) crystallography at synchrotron and X-ray free-electron laser (XFEL) sources distributes the absorbed radiation dose over all crystals used for data collection and therefore allows measurement of radiation damage prone systems, including the use of microcrystals for room-temperature measurements. Serial crystallography relies on fast and efficient exchange of crystals upon X-ray exposure, which can be achieved using a variety of methods, including various injection techniques. The latter vary significantly in their flow rates - gas dynamic virtual nozzle based injectors provide very thin fast-flowing jets, whereas high-viscosity extrusion injectors produce much thicker streams with flow rates two to three orders of magnitude lower. High-viscosity extrusion results in much lower sample consumption, as its sample delivery speed is commensurate both with typical XFEL repetition rates and with data acquisition rates at synchrotron sources. An obvious viscous injection medium is lipidic cubic phase (LCP) as it is used for in meso membrane protein crystallization. However, LCP has limited compatibility with many crystallization conditions. While a few other viscous media have been described in the literature, there is an ongoing need to identify additional injection media for crystal embedding. Critical attributes are reliable injection properties and a broad chemical compatibility to accommodate samples as heterogeneous and sensitive as protein crystals. Here, the use of two novel hydro-gels as viscous injection matrices is described, namely sodium carb-oxy-methyl cellulose and the thermo-reversible block polymer Pluronic F-127. Both are compatible with various crystallization conditions and yield acceptable X-ray background. The stability and velocity of the extruded stream were also analysed and the dependence of the stream velocity on the flow rate was measured. In contrast with previously characterized injection media, both new matrices afford very stable adjustable streams suitable for time-resolved measurements.

Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.

Dynamic fracture of tantalum under extreme tensile stress

The understanding of fracture phenomena of a material at extremely high strain rates is a key issue for a wide variety of scientific research ranging from applied science and technological developments to fundamental science such as laser-matter interaction and geology. Despite its interest, its study relies on a fine multiscale description, in between the atomic scale and macroscopic processes, so far only achievable by large-scale atomic simulations. Direct ultrafast real-time monitoring of dynamic fracture (spallation) at the atomic lattice scale with picosecond time resolution was beyond the reach of experimental techniques. We show that the coupling between a high-power optical laser pump pulse and a femtosecond x-ray probe pulse generated by an x-ray free electron laser allows detection of the lattice dynamics in a tantalum foil at an ultrahigh strain rate of [Formula: see text] ~2 × 10⁸ to 3.5 × 10⁸ s^-1. A maximal density drop of 8 to 10%, associated with the onset of spallation at a spall strength of ~17 GPa, was directly measured using x-ray diffraction. The experimental results of density evolution agree well with large-scale atomistic simulations of shock wave propagation and fracture of the sample. Our experimental technique opens a new pathway to the investigation of ultrahigh strain-rate phenomena in materials at the atomic scale, including high-speed crack dynamics and stress-induced solid-solid phase transitions.

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm³ in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm³ in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

Orientational order of liquids and glasses via fluctuation diffraction

Liquids, glasses and other amorphous matter lack long-range order, which makes them notoriously difficult to study. Local atomic order is partially revealed by measuring the distribution of pairwise atomic distances, but this measurement is insensitive to orientational order and unable to provide a complete picture of diverse amorphous phenomena, such as supercooling and the glass transition. Fluctuation scattering with electrons and X-rays is able provide this orientational sensitivity, but it is difficult to obtain clear structural interpretations of fluctuation data. Here we show that the interpretation of fluctuation diffraction data can be simplified by converting it into a real-space angular distribution function. We calculate this function from simulated diffraction of amorphous nickel, generated with a classical molecular dynamics simulation of the quenching of a high temperature liquid state. We compare the results of the amorphous case to the initial liquid state and to the ideal f.c.c. lattice structure of nickel. We show that the extracted angular distributions are rich in information about orientational order and bond angles. The diffraction fluctuations are potentially measurable with electron sources and also with the brightest X-ray sources, like X-ray free-electron lasers.

Structure Determination Using X-Ray Free-Electron Laser Pulses

The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to macromolecular crystals by several orders of magnitude higher than usually tolerable in conventional measurements, allowing crystal size to be decreased dramatically in diffraction measurements and without the need to cool the sample. Such pulses lead to the eventual vaporization of the sample, which has required a measurement approach, called serial crystallography, of consolidating snapshot diffraction patterns of many individual crystals. This in turn has further separated the connection between dose and obtainable diffraction information, with the only requirement from a single pattern being that to give enough information to place it, in three-dimensional reciprocal space, in relation to other patterns. Millions of extremely weak patterns can be collected and combined in this way, requiring methods to rapidly replenish the sample into the beam while generating the lowest possible background . The method is suited to time-resolved measurements over timescales below 1 ps to several seconds, and opens new opportunities for phasing. Some straightforward considerations of achievable signal levels are discussed and compared with a wide variety of recent experiments carried out at XFEL, synchrotron, and even laboratory sources, to discuss the capabilities of these new approaches and give some perspectives on their further development.

Design of a prototype split-and-delay unit for XFEL pulses, and their evaluation by synchrotron radiation X-rays

A prototype split-and-delay unit (SDU) for X-ray free-electron laser (XFEL) pulses is proposed based on the Graeff-Bonse four-Bragg-reflection interferometer by installing 12.5° slopes. The SDU can continuously provide a delay time from approximately -20 to 40 ps with a resolution of less than 26 fs. Because the SDU was constructed from a monolithic silicon crystal, alignment is straightforward. The obtained thoroughputs of the SDU reached 0.7% at 7.46 keV and 0.02% at 14.92 keV. The tunability of the delay time using the proposed SDU was demonstrated by finding the interference effects of the split X-rays, and the time resolution of the proposed SDU was evaluated using the width of the interference pattern recorded on the X-ray charge-coupled device camera by changing the energy, i.e. longitudinal coherence length, of the incident X-rays. It is expected that the proposed SDU will be applicable to XFEL experiments using delay times from tens of femtoseconds to tens of picoseconds, e.g. intensity correlation measurements.

Oxygen additions in serial femtosecond crystallographic protein structures

In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation-induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R-factors of the resulting structural model.

Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals

Second harmonic generation correlation spectroscopy (SHG-CS) is demonstrated as a new approach to protein nanocrystal characterization. A novel line-scanning approach was performed to enable autocorrelation analysis without sample damage from the intense incident beam. An analytical model for autocorrelation was developed, which includes a correction for the optical scattering forces arising when focusing intense, infrared beams. SHG-CS was applied to the analysis of BaTiO3 nanoparticles ranging from 200 to ∼500 nm and of photosystem I nanocrystals. A size distribution was recovered for each sample and compared with the size histogram measured by scanning electron microscopy (SEM). Good agreement was observed between the two independent measurements. The intrinsic selectivity of the second-order nonlinear optical process provides SHG-CS with the ability to distinguish well ordered nanocrystals from conglomerates and amorphous aggregates. Combining the recovered distribution of particle diameters with the histogram of measured SHG intensities provides the inherent hyperpolarizability per unit volume of the SHG-active nanoparticles. Simulations suggest that the SHG activity per unit volume is likely to exhibit relatively low sensitivity to the subtle distortions within the lattice that contribute to resolution loss in X-ray diffraction, but high sensitivity to the presence of multi-domain crystals.