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Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light. Plants adapt to the availability of light throughout their lives because it regulates so many aspects of their growth and reproduction. To detect the level of light, plant cells use proteins called phytochromes, which are also found in some bacteria and fungi. Phytochrome proteins change shape when they are exposed to red light, and this change alters the behaviour of the cell. The red light is absorbed by a molecule known as chromophore, which is connected to a region of the phytochrome called the PHY-tongue. This region undergoes one of the key structural changes that occur when the phytochrome protein absorbs light, turning from a flat sheet into a helix. Claesson, Wahlgren, Takala et al. studied the structure of a bacterial phytochrome protein almost immediately after shining a very brief flash of red light using a laser. The experiments revealed that the structure of the protein begins to change within a trillionth of a second: specifically, the chromophore twists, which disrupts its attachment to the protein, freeing the protein to change shape. Claesson, Wahlgren, Takala et al. note that this structure is likely a very short-lived intermediate state, which however triggers more changes in the overall shape change of the protein. One feature of the rearrangement is the disappearance of a particular water molecule. This molecule can be found at the core of many different phytochrome structures and interacts with several parts of the chromophore and the phytochrome protein. It is unclear why the water molecule is lost, but given how quickly this happens after the red light is applied it is likely that this disappearance is an integral part of the reshaping process. Together these events disrupt the interactions between the chromophore and the PHY-tongue, enabling the PHY-tongue to change shape and alter the structure of the phytochrome protein. Understanding and controlling this process could allow scientists to alter growth patterns in plants, such as crops or weeds.

Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.

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 fromX-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.

Serial femtosecond X‐ray crystallography (SFX) captures the structure and dynamics of biological macromolecules at high spatial and temporal resolutions. The ultrashort pulse produced by an X‐ray free‐electron laser (XFEL) `outruns' much of the radiation damage that impairs conventional crystallography. However, the rapid onset of `electronic damage' due to ionization limits this benefit. Here, we distinguish the influence of different atomic species on the ionization of protein crystals by employing a plasma code that tracks the unbound electrons as a continuous energy distribution. The simulations show that trace quantities of heavy atoms (Z > 10) contribute a substantial proportion of global radiation damage by rapidly seeding electron ionization cascades. In a typical protein crystal, sulfur atoms and solvated salts induce a substantial fraction of light‐atom ionization. In further modeling of various targets, global ionization peaks at photon energies roughly 2 keV above inner‐shell absorption edges, where sub‐2 keV photoelectrons ejected from these shells initiate ionization cascades that are briefer than the XFEL pulse. These results indicate that relatively small quantities of heavy elements can substantially affect global radiation damage in XFEL experiments. Plasma simulations with detailed modeling of unbound electron dynamics predict that heavy elements contribute significantly to radiation damage suffered by proteins in serial femtosecond crystallography. New methods to mitigate radiation damage in this regime are highlighted.

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.

X-ray crystallographic methods can be used to visualize macromolecules at high resolution. This provides an understanding of molecular mechanisms and an insight into drug development and rational engineering of enzymes used in the industry. Although conventional synchrotron-based X-ray crystallography remains a powerful tool for understanding molecular function, it has experimental limitations, including radiation damage, cryogenic temperature, and static structural information. Serial femtosecond crystallography (SFX) using X-ray free electron laser (XFEL) and serial millisecond crystallography (SMX) using synchrotron X-ray have recently gained attention as research methods for visualizing macromolecules at room temperature without causing or reducing radiation damage, respectively. These techniques provide more biologically relevant structures than traditional X-ray crystallography at cryogenic temperatures using a single crystal. Serial femtosecond crystallography techniques visualize the dynamics of macromolecules through time-resolved experiments. In serial crystallography (SX), one of the most important aspects is the delivery of crystal samples efficiently, reliably, and continuously to an X-ray interaction point. A viscous delivery medium, such as a carrier matrix, dramatically reduces sample consumption, contributing to the success of SX experiments. This review discusses the preparation and criteria for the selection and development of a sample delivery medium and its application for SX.

Advances in serial crystallography have reshaped approaches to radiation damage at room temperature. This commentary highlights recent work comparing XFEL and synchrotron experiments, emphasizing its implications for serial crystallography at modern X-ray sources.

Serial crystallography (SX) provides an opportunity to observe the molecular dynamics of macromolecular structures at room temperature via pump-probe studies. The delivery of crystals embedded in a viscous medium via an injector or syringe is widely performed in synchrotrons or X-ray free-electron laser facilities with low repetition rates. Various viscous media have been developed; however, there are cases in which the delivery material undesirably interacts chemically or biologically with specific protein samples, or changes the stability of the injection stream, depending on the crystallization solution. Therefore, continued discovery and characterization of new delivery media is necessary for expanding future SX applications. Here, the preparation and characterization of new polysaccharide (wheat starch (WS) and alginate)-based sample delivery media are introduced for SX. Crystals embedded in a WS or alginate injection medium showed a stable injection stream at a flow rate of < 200 nL/min and low-level X-ray background scattering similar to other hydrogels. Using these media, serial millisecond crystallography (SMX) was performed, and the room temperature crystal structures of glucose isomerase and lysozyme were determined at 1.9–2.0 Å resolutions. WS and alginate will allow an expanded application of sample delivery media in SX experiments.

Femtosecond optical measurements of photoexcitable molecular crystals carry ultrafast dynamics information with structural sensitivity. The creation and detection of transient dynamics depend on the optical parameters, as well as the explicit molecular structure, crystal symmetry, crystal orientation, polarisation of the photoexciting beam, and interaction geometry. In order to retrieve the linear and non-linear population transfer in photoexcited crystals, excitation theory is combined here with the calculation of birefringence decomposition and is shown for both the generalised uniaxial and biaxial systems. A computational tool was constructed based on this treatment to allow modelling of electric field decomposition, dipole projections, and non-linear excitation population levels. This is available open source and with a GUI for ease of use. Such work has applications in two areas of ultrafast science: multidimensional optical crystallography and femtosecond time-resolved X-ray crystallography.

Sheet-on-sheet (SOS) fixed-target chips are arguably the most versatile, cheapest and simplest sample-delivery method for ambient-temperature data acquisition using serial crystallography approaches at synchrotrons and X-ray free-electron lasers (XFELs). Their defining feature, the absence of any hard-patterned restrictions around crystals, is their strength as it removes limitations on crystal sizes or environments. However, it is also their weakness when it comes to limiting undesired effects on yet-to-be-irradiated crystals due to diffusing heat, radicals or gas originating from previous exposures. We explored whether SOS chips can be used for damage-free serial data collection on the new ID29 beamline at the ESRF-EBS, a fourth-generation synchrotron light source, as well as at the new Cristallina-MX station at SwissFEL. We collected serial data sets from microcrystals of the hemoprotein DtpAa, which was reported to have a highly radiation-sensitive iron–water bond length. The data sets differ in step size between exposures within and between lines of a serpentine-like data-acquisition scan. We observe no significant changes in the distance of the water ligand of the heme in the structures obtained from the ID29 SSX data. However, when compared with those collected at Cristallina-MX, the diffraction intensities collected at ID29 suggest global damage akin to Bragg termination occurring during the 90 µs exposure at ID29. Moreover, differences in the heme geometry and the proximal histidine–iron bond length point to local damage in all ID29 data sets regardless of the X-ray spacing. SFX data collected at Cristallina-MX show a phase transition of the DtpAa crystal lattice for X-ray step sizes of ≤20 µm. This phase transition might be caused by heating and/or hydrogen-gas-induced crystal dehydration. Vigilance remains required to safeguard against radiation damage at fourth-generation synchrotrons and XFELs.