Sample Delivery Media for Serial Crystallography

Synchrotron Radiation: A Key Tool for Drug Discovery

Synchrotron radiation is extensively utilized in the domains of materials science, physical chemistry, and life science, resulting from its high intensity, exceptional monochromaticity, superior collimation, and broad wave spectrum. This top-notch light source has also made significant contributions to the progress of biomedicine. The advancement of synchrotron radiation-based X-ray and protein crystallography technologies has created new prospects for drug discovery. These innovative techniques have opened up exciting avenues in the field. The investigation of protein crystal structures and the elucidation of the spatial configuration of biological macromolecules have revealed intricate details regarding the modes of protein binding. Furthermore, the screening of crystal polymorphs and ligands has laid the groundwork for rational drug modification and the improvement of drug physicochemical properties. As science and technology continue to advance, the techniques for analyzing structures using synchrotron radiation sources and the design of corresponding crystallographic beamline stations are undergoing continuous enhancement. These cutting-edge tools and facilities are expected to expedite the drug development process and rectify the current situation of a lack of targeted drugs.

Methods in molecular photocrystallography

Over the last three decades, the technology that makes it possible to follow chemical processes in the solid state in real time has grown enormously. These studies have important implications for the design of new functional materials for applications in optoelectronics and sensors. Light-matter interactions are of particular importance, and photocrystallography has proved to be an important tool for studying these interactions. In this technique, the three-dimensional structures of light-activated molecules, in their excited states, are determined using single-crystal X-ray crystallography. With advances in the design of high-power lasers, pulsed LEDs and time-gated X-ray detectors, the increased availability of synchrotron facilities, and most recently, the development of XFELs, it is now possible to determine the structures of molecules with lifetimes ranging from minutes down to picoseconds, within a single crystal, using the photocrystallographic technique. This review discusses the procedures for conducting successful photocrystallographic studies and outlines the different methodologies that have been developed to study structures with specific lifetime ranges. The complexity of the methods required increases considerably as the lifetime of the excited state shortens. The discussion is supported by examples of successful photocrystallographic studies across a range of timescales and emphasises the importance of the use of complementary analytical techniques in order to understand the solid-state processes fully.

Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography

Light-oxygen-voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.

Guide to serial synchrotron crystallography

Serial crystallography (SX) is an emerging technique that can be used to determine the noncryogenic crystal structure of macromolecules while minimizing radiation damage. Applying SX using pump-probe or mix-and-inject techniques enables the observation of time-resolved molecular reactions and dynamics in macromolecules. After the successful demonstration of the SX experimental technique with structure determination in serial femtosecond crystallography using an X-ray free electron laser, this method was adapted to the synchrotron, leading to the development of serial synchrotron crystallography (SSX). SSX offers new opportunities for researchers to leverage SX techniques, contributing to the advancement of structural biology and offering a deeper understanding of the structure and function of macromolecules. This review covers the background and advantages of SSX and its experimental approach. It also discusses important considerations when conducting SSX experiments.

Data of serial synchrotron crystallography of xylanase GH11 from Thermoanaerobacterium saccharolyticum

The endo-1,4-β-xylanase GH11 from the hemicellulose-degrading bacterium Thermoanaerobacterium saccharolyticum (TsaGH11) has been characterized as a thermophilic enzyme. TsaGH11 exhibits its maximum activity at pH 5.0 and 70 °C, along with superior properties towards beechwood xylan, with a Km of 12.9 mg mL⁻¹ and a Kcat of 34,015.3 s⁻¹. The room-temperature and cryogenic crystal structures of TsaGH11 were determined using serial synchrotron crystallography (SSX) and conventional macromolecular crystallography techniques, respectively. The high-resolution crystal structure of TsaGH11 was successfully determined, and the flexibility of the thumb domain at room temperature was elucidated. During SSX data collection, a high density of crystal samples in the sample holder led to an unprecedentedly high multi-crystal hit rate of ∼200 %. Data containing these multi-crystal hits will potentially be a valuable resource for developing indexing algorithms for multi-crystal hit patterns in serial crystallography (SX) data processing. To contribute to developing SX data processing, this paper provides detailed and specific information about the data collection and processing of TsaGH11 obtained through SSX experiments.

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.

All polymer microfluidic chips-A fixed target sample delivery workhorse for serial crystallography

The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around "workhorse" for serial crystallography measurements. This Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.

Research Progress of Immunomodulation on Anti-COVID-19 and the Effective Components from Traditional Chinese Medicine

SARS-CoV-2 has posed a threat to the health of people around the world because of its strong transmission and high virulence. Currently, there is no specific medicine for the treatment of COVID-19. However, for a wide variety of medicines used to treat COVID-19, traditional Chinese medicine (TCM) plays a major role. In this paper, the effective treatment of COVID-19 using TCM was consulted first, and several Chinese medicines that were frequently used apart from their huge role in treating it were found. Then, when exploring the active ingredients of these herbs, it was discovered that most of them contained flavonoids. Therefore, the structure and function of the potential active substances of flavonoids, including flavonols, flavonoids, and flavanes, respectively, are discussed in this paper. According to the screening data, these flavonoids can bind to the key proteins of SARS-CoV-2, 3CLpro, PLpro, and RdRp, respectively, or block the interface between the viral spike protein and ACE2 receptor, which could inhibit the proliferation of coronavirus and prevent the virus from entering human cells. Besides, the effects of flavonoids on the human body systems are expounded on in this paper, including the respiratory system, digestive system, and immune system, respectively. Normally, flavonoids boost the body's immune system. However, they can suppress the immune system when over immunized. Ultimately, this study hopes to provide a reference for the clinical drug treatment of COVID-19 patients, and more TCM can be put into the market accordingly, which is expected to promote the development of TCM on the international stage.

Combination of an inject-and-transfer system for serial femtosecond crystallography

Serial femtosecond crystallography (SFX) enables the determination of room-temperature crystal structures of macromolecules with minimized radiation damage and provides time-resolved molecular dynamics by pump-probe or mix-and-inject experiments. In SFX, a variety of sample delivery methods with unique advantages have been developed and applied. The combination of existing sample delivery methods can enable a new approach to SFX data collection that combines the advantages of the individual methods. This study introduces a combined inject-and-transfer system (BITS) method for sample delivery in SFX experiments: a hybrid injection and fixed-target scanning method. BITS allows for solution samples to be reliably deposited on ultraviolet ozone (UVO)-treated polyimide films, at a minimum flow rate of 0.5 nl min-1, in both vertical and horizontal scanning modes. To utilize BITS in SFX experiments, lysozyme crystal samples were embedded in a viscous lard medium and injected at flow rates of 50-100 nl min-1 through a syringe needle onto a UVO-treated polyimide film, which was mounted on a fixed-target scan stage. The crystal samples deposited on the film were raster scanned with an X-ray free electron laser using a motion stage in both horizontal and vertical directions. Using the BITS method, the room-temperature structure of lysozyme was successfully determined at a resolution of 2.1 Å, and thus BITS could be utilized in future SFX experiments.

Preliminary XFEL data from spontaneously grown endo-1,4-β-xylanase crystals from Hypocrea virens

The enzymatic degradation of semi-cellulosic substrates has recently received immense attention. The enzyme endo-1,4-β-xylanase is essential for the complete digestion of complex and heterogeneous hemicellulose. Here, the purification, crystallization and preliminary X-ray free-electron laser (XFEL) diffraction analysis of endo-1,4-β-xylanase from the fungus Hypocrea virens (HviGH11) are reported. Codon-optimized HviGH11 was overexpressed in Escherichia coli and spontaneously crystallized after His-tag purification and concentration. Preliminary XFEL diffraction data were collected at the Pohang Accelerator Laboratory XFEL (PAL-XFEL). A total of 1021 images containing Bragg peaks were obtained and indexed. The HviGH11 crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 43.80, b = 51.90, c = 94.90 Å. Using 956 diffraction patterns, the phasing problem was solved and an initial model structure of HviGH11 was obtained.

Beef tallow injection matrix for serial crystallography

Serial crystallography (SX) enables the visualization of the time-resolved molecular dynamics of macromolecular structures at room temperature while minimizing radiation damage. In SX experiments, the delivery of a large number of crystals into an X-ray interaction point in a serial and stable manner is key. Sample delivery using viscous medium maintains the stable injection stream at low flow rates, markedly reducing sample consumption compared with that of a liquid jet injector and is widely applied in SX experiments with low repetition rates. As the sample properties and experimental environment can affect the stability of the injection stream of a viscous medium, it is important to develop sample delivery media with various characteristics to optimize the experimental environment. In this study, a beef tallow injection matrix possessing a higher melting temperature than previously reported fat-based shortening and lard media was introduced as a sample delivery medium and applied to SX. Beef tallow was prepared by heat treating fats from cattle, followed by the removal of soluble impurities from the extract by phase separation. Beef tallow exhibited a very stable injection stream at room temperature and a flow rate of < 10 nL/min. The room-temperature structures of lysozyme and glucose isomerase embedded in beef tallow were successfully determined at 1.55 and 1.60 Å, respectively. The background scattering of beef tallow was higher than that of previously reported fat-based shortening and lard media but negligible for data processing. In conclusion, the beef tallow matrix can be employed for sample delivery in SX experiments conducted at temperatures exceeding room temperature.

Serial X-ray Crystallography

Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.

Processing of Multicrystal Diffraction Patterns in Macromolecular Crystallography Using Serial Crystallography Programs

Cryocrystallography is a widely used method for determining the crystal structure of macromolecules. This technique uses a cryoenvironment, which significantly reduces the radiation damage to the crystals and has the advantage of requiring only one crystal for structural determination. In standard cryocrystallography, a single crystal is used for collecting diffraction data, which include single-crystal diffraction patterns. However, the X-ray data recorded often may contain diffraction patterns from several crystals. The indexing of multicrystal diffraction patterns in cryocrystallography requires more precise data processing techniques and is therefore time consuming. Here, an approach for processing multicrystal diffraction data using a serial crystallography program is introduced that allows for the integration of multicrystal diffraction patterns from a single image. Multicrystal diffraction data were collected from lysozyme crystals and processed using the serial crystallography program CrystFEL. From 360 images containing multicrystal diffraction patterns, 1138 and 691 crystal lattices could be obtained using the XGANDALF and MOSFLM indexing algorithms, respectively. Using this indexed multi-lattice information, the crystal structure of the lysozyme could be determined successfully at a resolution of 1.9 Å. Therefore, the proposed approach, which is based on serial crystallography, is suitable for processing multicrystal diffraction data in cryocrystallography.

Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX

CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open-close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono-acyl-glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy-droxy-propyl methyl-cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.

Stable sample delivery in a viscous medium via a polyimide-based single-channel microfluidic chip for serial crystallography

Serial crystallography (SX) provides room-temperature crystal structures with minimal radiation damage and facilitates the comprehension of molecular dynamics through time-resolved studies. In SX experiments, it is important to deliver a large number of crystal samples to the X-ray interaction point in a serial and stable manner. The advantage of crystal delivery in a viscous medium via a capillary is the ability to deliver all of the crystal samples to the X-ray interaction point at a low flow rate; however, the capillary often breaks during handling and high X-ray absorption can occur at low energy states. This study aimed to develop a stable system for sample delivery in a viscous medium via a polyimide-based single-channel microfluidic (PSM) chip for SX. Since this microfluidic chip comprises a polyimide film, it has high tensile strength and higher X-ray transmittance than a quartz capillary. The PSM chip was connected to a syringe containing the microcrystals embedded in viscous medium. The channel of the PSM chip was aligned to the X-ray path, and the viscous medium containing lysozyme crystals was stably delivered using a syringe pump at a flow rate of 100 nl min−1. Room-temperature lysozyme crystal structures were successfully determined at 1.85 Å resolution. This method would greatly facilitate sample delivery for SX experiments using synchrotron X-rays.

Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography

The serial crystallography (SX) technique enables the determination of the room-temperature structure of a macromolecule while causing minimal radiation damage, as well as the visualization of the molecular dynamics by time-resolved studies. The fixed-target (FT) scanning approach is one method for SX sample delivery that minimizes sample consumption and minimizes physical damage to crystals during data collection. Settling of the crystals on the sample holder in random orientation is important for complete three dimensional data collection. To increase the random orientation of crystals on the sample holder, we developed a polyimide mesh-based sample holder with irregular crystal mounting holes for FT-SX. The polyimide mesh was fabricated using a picosecond laser. Each hole in the polyimide mesh has irregularly shaped holes because of laser thermal damage, which may cause more crystals to settle at random orientations compared to regular shaped sample holders. A crystal sample was spread onto a polyimide-mesh, and a polyimide film was added to both sides to prevent dehydration. Using this sample holder, FT-SX was performed at synchrotron and determined the room-temperature lysozyme structure at 1.65 Å. The polyimide mesh with irregularly shaped holes will allow for expanded applications in sample delivery for FT-SX experiments.

Approach of Serial Crystallography II

Serial crystallography (SX) is an emerging X-ray crystallographic method for determining macromolecule structures. It can address concerns regarding the limitations of data collected by conventional crystallography techniques, which require cryogenic-temperature environments and allow crystals to accumulate radiation damage. Time-resolved SX studies using the pump-probe methodology provide useful information for understanding macromolecular mechanisms and structure fluctuation dynamics. This Special Issue deals with the serial crystallography approach using an X-ray free electron laser (XFEL) and synchrotron X-ray source, and reviews recent SX research involving synchrotron use. These reports provide insights into future serial crystallography research trends and approaches.

Advancements in macromolecular crystallography: from past to present

Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.

Tuning Transport Phenomena in Agarose Gels for the Control of Protein Nucleation Density and Crystal Form

Agarose gels provide the ideal environment for studying the nucleation step of complex biomacromolecules under diffusion-controlled conditions. In the present paper, we characterized the influence of agarose on the nucleation of three model proteins, i.e., lysozyme, insulin, and proteinase K, as a function of the agarose concentration using a batch method set-up inside flat capillaries. By using this set-up, we were able to directly count the number of crystals in a given volume and correlate it with the amount of agarose and with the average crystal size. We also studied the crystallization behavior of proteinase K with free-interface diffusion so that batch conditions were achieved through slow diffusion of the precipitant. Thanks to the control over the protein mass transport imposed by the network, a previously unknown crystal form, P212121, was obtained, and the three-dimensional structure was determined at a 1.6 Å resolution. Overall, the versatility of agarose gels makes them ideal candidates for the preparation of microcrystalline suspensions of biopharmaceuticals with precise and reproducible crystal attributes or for the exploration of the existence of different polymorphs.

Room-Temperature Structure of Xylitol-Bound Glucose Isomerase by Serial Crystallography: Xylitol Binding in the M1 Site Induces Release of Metal Bound in the M2 Site

Glucose isomerase (GI) is an important enzyme that is widely used in industrial applications, such as in the production of high-fructose corn syrup or bioethanol. Studying inhibitor effects on GI is important to deciphering GI-specific molecular functions, as well as potential industrial applications. Analysis of the existing xylitol-bound GI structure revealed low metal occupancy at the M2 site; however, it remains unknown why this phenomenon occurs. This study reports the room-temperature structures of native and xylitol-bound GI from Streptomyces rubiginosus (SruGI) determined by serial millisecond crystallography. The M1 site of native SruGI exhibits distorted octahedral coordination; however, xylitol binding results in the M1 site exhibit geometrically stable octahedral coordination. This change results in the rearrangement of metal-binding residues for the M1 and M2 sites, the latter of which previously displayed distorted metal coordination, resulting in unstable coordination of Mg²⁺ at the M2 site and possibly explaining the inducement of low metal-binding affinity. These results enhance the understanding of the configuration of the xylitol-bound state of SruGI and provide insights into its future industrial application.

Molecular Dynamics-From Small Molecules to Macromolecules

All molecular systems, from small molecules to macromolecules, exhibit specific characteristics for a specific environment and time. In order to gain an accurate understanding of the functions of all types of molecules, studies of their structure and dynamics are essential. Through dynamic studies, using techniques such as spectroscopy, structure determination, and computer analysis, it is possible to collect functional information on molecules at specific times and in specific environments. Such information not only reveals the properties and mechanisms of action of molecules but also provides insights that can be applied to various industries, such as the development of new materials and drugs. Herein, I discuss the importance of molecular dynamics studies, present the time scale of molecular motion, and review techniques for analyzing molecular dynamics.

The XBI BioLab for life science experiments at the European XFEL

The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.

Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center

With the recent developments in the field of free-electron-laser-based serial femtosecond crystallography, the necessity to obtain a large number of high-quality crystals has emerged. In this work crystallization techniques were selected, tested and optimized for the lipid mesophase crystallization of the Rhodobacter sphaeroides membrane pigment-protein complex, known as the photosynthetic reaction center (RC). Novel approaches for lipid sponge phase crystallization in comparatively large volumes using Hamilton gas-tight glass syringes and plastic pipetting tips are described. An analysis of RC crystal structures obtained by lipid mesophase crystallization revealed non-native ligands that displaced the native electron-transfer cofactors (carotenoid sphero-idene and a ubi-quinone molecule) from their binding pockets. These ligands were identified and were found to be lipids that are major mesophase components. The selection of distinct co-crystallization conditions with the missing cofactors facilitated the restoration of sphero-idene in its binding site.

Approach of Serial Crystallography

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder

Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target scanning approach has the advantage of dramatically minimizing sample consumption as well as any physical damage to crystal sample, compared to other sample delivery methods. Here, we introduce the simple approach of fixed-target serial synchrotron crystallography (FT-SSX) using nylon mesh and enclosed film (NAM)-based sample holder. The NAM-based sample holder consisted of X-ray-transparent nylon-mesh and polyimide film, attached to a magnetic base. This sample holder was mounted to a goniometer head on macromolecular crystallography beamline, and translated along vertical and horizontal directions for raster scanning by the goniometer. Diffraction data were collected in two raster scanning approaches: (i) 100 ms X-ray exposure and 0.011° oscillation at each scan point and (ii) 500 ms X-ray exposure and 0.222° oscillation at each scan point. Using this approach, we determined the room-temperature crystal structures of lysozyme and glucose isomerase at 1.5–2.0 Å resolution. The sample holder produced negligible X-ray background scattering for data processing. Therefore, the new approach provided an opportunity to perform FT-SSX with high accessibility using macromolecular crystallography beamlines at synchrotron without any special equipment.

Lard Injection Matrix for Serial Crystallography

Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject experiments. Delivering a crystal sample using a viscous medium decreases sample consumption by lowering the flow rate while being extruded from the injector or syringe as compared to a liquid jet injector. Since the environment of crystal samples varies, continuous development of the delivery medium is important for extended SX applications. Herein, I report the preparation and characterization of a lard-based sample delivery medium for SX. This material was obtained using heat treatment, and then the soluble impurities were removed through phase separation. The lard injection medium was highly stable and could be injected via a syringe needle extruded at room temperature with a flow rate < 200 nL/min. Serial millisecond crystallography experiments were performed using lard, and the room temperature structures of lysozyme and glucose isomerase embedded in lard at 1.75 and 1.80 Å, respectively, were determined. The lard medium showed X-ray background scattering similar or relatively lower than shortenings and lipidic cubic phase; therefore, it can be used as sample delivery medium in SX experiments.

Viscous-medium-based crystal support in a sample holder for fixed-target serial femtosecond crystallography

Serial femtosecond crystallography (SFX) enables the determination of the room-temperature crystal structure of macromolecules, as well as providing time-resolved molecular dynamics data in pump–probe experiments. Fixed-target SFX (FT-SFX) can minimize sample consumption and physical effects on crystals during sample delivery. In FT-SFX studies, having a sample holder that can stably fix crystal samples is one of the key elements required for efficient data collection. Hence, development of sample holders from new materials capable of supporting various crystal sizes and shapes may expand the applications of FT-SFX. Here, a viscous-media-based crystal support in a sample holder for FT-SFX is introduced. Crystal samples were embedded in viscous media, namely gelatin and agarose, which were enclosed in a polyimide film. In the vertically placed sample holder, 10–15%(w/v) viscous gelatin and 1–4%(w/v) agarose gel stably supported crystals between two polyimide films, thereby preventing the crystals from descending owing to gravity. Using this method, FT-SFX experiments were performed with glucose isomerase and lysozyme embedded in gelatin and agarose, respectively. The room-temperature crystal structures of glucose isomerase and lysozyme were successfully determined at 1.75 and 1.80 Å resolutions, respectively. The glucose isomerase and lysozyme diffraction analyses were not impeded by excessive background scattering from the viscous media. This method is useful for delivering crystal samples of various sizes and shapes in FT-SFX experiments.

Polysaccharide-Based Injection Matrix for Serial Crystallography

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.

Towards an Optimal Sample Delivery Method for Serial Crystallography at XFEL

The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.

Stable sample delivery in viscous media via a capillary for serial crystallography

Serial crystallography (SX) is an innovative technology in structural biology that enables the visualization of the molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample-delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques, drastically reducing sample consumption. In serial millisecond crystallography using a viscous medium via a capillary, crystals of lysozyme embedded in agarose, which produce an unstable injection stream at atmospheric pressure, and crystals of glucose isomerase embedded in gelatin, which is known to be problematic for open-extruder operation, were stably delivered at a flow rate of 100 nl min−1. The room-temperature crystal structures of lysozyme and glucose isomerase were successfully determined at 1.85 and 1.70 Å resolutions, respectively. This simple but highly efficient sample-delivery method can allow researchers to deliver crystals precisely to an X-ray beam in SX experiments.

Shortening injection matrix for serial crystallography

Serial crystallography allows crystal structures to be determined at room temperature through the steady delivery of crystals to the X-ray interaction point. Viscous delivery media are advantageous because they afford efficient sample delivery from an injector or syringe at a low flow rate. Hydrophobic delivery media, such as lipidic cubic phase (LCP) or grease, provide a stable injection stream and are widely used. The development of new hydrophobic delivery materials can expand opportunities for future SX studies with various samples. Here, I introduce fat-based shortening as a delivery medium for SX experiments. This material is commercially available at low cost and is straightforward to handle because its phase (i.e., solid or liquid) can be controlled by temperature. Shortening was extruded from a syringe needle in a stable injection stream even below 200 nl/min. X-ray exposed shortening produced several background scattering rings, which have similar or lower intensities than those of LCP and contribute negligibly to data processing. Serial millisecond crystallography was performed using two shortening delivery media, and the room temperature crystal structures of lysozyme and glucose isomerase were successfully determined at resolutions of 1.5–2.0 Å. Therefore, shortening can be used as a sample delivery medium in SX experiments.

Sample delivery using viscous media, a syringe and a syringe pump for serial crystallography

Sample delivery using injectors is widely used in serial crystallography (SX) and has significantly contributed to the determination of crystal structures at room temperature. However, sophisticated injector nozzle fabrication methods and sample delivery operations have made it difficult for ordinary users to access the SX research. Herein, a simple and easily accessible sample delivery method for SX experiments is introduced, that uses a viscous medium, commercially available syringe and syringe pump. The syringe containing the lysozyme crystals embedded in lipidic cubic phase (LCP) or polyacrylamide (PAM) delivery media was connected to a needle having an inner diameter of 168 µm, after which it was installed on a syringe pump. By driving the syringe pump, the syringe plunger was pushed and the crystal sample was delivered to the X-ray beam position in a stable manner. Using this system, the room-temperature crystal structures of lysozyme embedded in LCP and PAM at 1.56 Å and 1.75 Å, respectively, were determined. This straightforward syringe pump-based sample delivery system can be utilized in SX.

The serial millisecond crystallography instrument at the Australian Synchrotron incorporating the "Lipidico" injector

A serial millisecond crystallography (SMX) facility has recently been implemented at the macromolecular crystallography beamline, MX2 at the Australian Synchrotron. The setup utilizes a combination of an EIGER X 16M detector system and an in-house developed high-viscosity injector, "Lipidico." Lipidico uses a syringe needle to extrude the microcrystal-containing viscous media and it is compatible with commercially available syringes. The combination of sample delivery via protein crystals suspended in a viscous mixture and a millisecond frame rate detector enables high-throughput serial crystallography at the Australian Synchrotron. A hit-finding algorithm, based on the principles of "robust-statistics," is employed to rapidly process the data. Here we present the first SMX experimental results with a detector frame rate of 100 Hz (10 ms exposures) and the Lipidico injector using a mixture of lysozyme microcrystals embedded in high vacuum silicon grease. Details of the experimental setup, sample injector, and data analysis pipeline are designed and developed as part of the Australian Synchrotron SMX instrument and are reviewed here.

The XFEL Protein Crystallography: Developments and Perspectives

In the past 10 years, the world has witnessed the revolutionary development of X-ray free electron lasers (XFELs) and their applications in many scientific disciplinaries [...].

Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography

Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage. Despite a number of advantages, preparation of a sample holder for the sample delivery in FT-SFX with the use of many crystals in a single mount at ambient temperature is challenging as it can be complicated and costly, and thus, development of an efficient sample holder is essential. In this study, we introduced a nylon mesh-based sample holder enclosed by a polyimide film. This sample holder can be rapidly manufactured using a commercially available nylon mesh with pores of a desired size at a low cost without challenging technology. Furthermore, this simple device is highly efficient in data acquisition. We performed FT-SFX using a nylon mesh-based sample holder and collected over 130,000 images on a single sample holder using a 30 Hz X-ray pulse for 1.2 h. We determined the crystal structures of lysozyme and glucose isomerase using the nylon mesh at 1.65 and 1.75 Å, respectively. The nylon mesh exposed to X-rays produced very low levels of background scattering at 3.75 and 4.30 Å, which are negligible for data analysis. Our method provides a simple and rapid but highly efficient way to deliver samples for FT-SFX.