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Single crystal X-ray diffraction application notes

Product line: Protein, Single crystal
Application number Title Body Product name Industries
PX015 Data collection and improved spot resolution with the HyPix-6000HE HPC detector The HyPix-6000HE hybrid photon counting (HPC) detector is the latest detector for protein data collection designed by Rigaku. The HyPix-6000HE detector possesses all the benefits associated with HPC detectors: high sensitivity, large dynamic range, very low read noise, single pixel point-spread function and shutterless data collection. In addition, the HyPix-6000HE also features a small pixel size of 100 μm x 100 μm and a frame rate of 100 Hz. The small pixel size of the HyPix-6000HE facilitates improved spatial resolution for reflections from crystals with long unit cell axes, and enables data collection with shorter detector distances. HyPix-6000HE Academic research, Pharmaceuticals
PX019 Catalase data collection & 1.7 Å structure We have collected data on a catalase crystal using the EIGER R 4M and solved its structure to 1.7 Å. EIGER R series Academic research, Pharmaceuticals
PX020 In-situ Data Collection and Structure Solution Using the XtalCheck-S System With the XtalCheck-S system, one eliminates the need to harvest and cryo-protect samples and, thus, can quickly and easily survey many crystallization experiments. In-plate screening has the added advantage that it reduces the risk of damaging fragile or sensitive crystals by eliminating the need to remove them from mother liquor for X-ray data collection. Moreover, one can perform complete crystallography experiments by collecting data from multiple crystals in random orientations to achieve a complete set of reflection that can be used for structure solution. XtalCheck-S Academic research, Pharmaceuticals
PX021 I-SAD phasing of the HIV integrase core domain using data collected on the XtaLAB Synergy-S The XtaLAB Synergy-S is our microfocus sealed-tube 4-circle diffractometer for small molecule and macromolecular crystallography. It features three new technologies in a compact cabinet that will fit into any home laboratory: microfocus PhotonJet-S sources (with Cu, Mo, or Ag targets), an ultrafast (10 degrees per second) Kappa goniometer, and a HyPix-6000HE hybrid photon counting detector with 0.1 mm by 0.1 mm pixels. Here, we collected an overnight data set on a crystal of the HIV integrase core domain (IN) to demonstrate iodine SAD phasing on a real-world laboratory sample. XtaLAB Synergy-S Academic research, Pharmaceuticals
PX022 Thaumatin S-SAD phasing with 2 hours of data collection on the XtaLAB Synergy-S We recently introduced a sealed-tube 4-circle diffractometer for small molecule and macromolecular crystallography, the XtaLAB Synergy-S. It features three new technologies in a compact cabinet that will fit into any home laboratory: microfocus PhotonJet-S sources (with Cu, Mo, or Ag targets), an ultrafast (10 degrees per second) Kappa goniometer, and a HyPix-6000HE hybrid photon counting detector with 0.1 mm by 0.1 mm pixels. Here, we collected a two-hour data set on a thaumatin crystal to demonstrate the quality of data from the XtaLab Synergy-S system using a protein crystal with an average size unit cell. XtaLAB Synergy-S Academic research, Pharmaceuticals
PX023 ClpS SAD phasing


Rigaku’s XtaLAB Synergy-S is much more than a crystal screening instrument. It comes equipped with a powerful source, an ultrafast kappa goniometer, and a hybrid photon counting detector to enable fast data collections on macromolecular crystals. Here, we show a 30-minute data collection on an orthorhombic crystal of ClpS. The data are complete to 1.28 Å and the structure can be solved by single wavelength anomalous dispersion (SAD).

XtaLAB Synergy-S Academic research, Chemistry, Materials science
PX024 Lysozyme S-SAD phasing


A modern, home laboratory X-ray diffraction system with the latest in photon counting detector technology should deliver high quality data in a short amount of time. Rigaku Oxford Diffraction currently promotes the XtaLAB Synergy Custom outfitted with a MicroMax-007HF rotating Cu anode, VariMax optics, ultrafast Kappa goniometer, and a HyPix-6000HE hybrid photon counting detector as the gold standard for a home laboratory X-ray diffraction system. To back up that claim, we present here the results of a 2.25-minute data collection on a 0.2 mm lysozyme crystal along with the sulfur SAD

XtaLAB Synergy Custom Chemistry
PX026 Sulfur SAD phasing of thaumatin in 10 minutes This note demonstrates fast S-SAD phasing of T. danielli Thaumatin. XtaLAB Synergy-DW VHF, HyPix-Arc 150° Pharmaceuticals, Academic research
PX028 Resolving large unit cells by using the correct detector, distance, and beam divergence


Large unit cells pose a challenge for any home lab diffractometer equipped with modern, high-flux confocal multilayer optics with a small beam size (≤ 100 μm). The larger the unit cell, the closer the reflections are to each other on a diffraction image. To minimize overlap and resolve these reflections as separate peaks, one usually increases the crystal-to-detector distance, but larger distances result in enlarged reflections due to the divergence of the X-ray beam. Therefore, adjustable divergence on the optics is critical. Here, we will show the screening, data collection and

XtaLAB Synergy Custom Chemistry
PX029 Introducing the XtaLAB Synergy Flow The XtaLAB Synergy Flow turns any XtaLAB Synergy cabinet diffractometer into an automated, high-throughput machine by incorporating a 6-axis UR3 Universal Robot and a 3-puck dewar. XtaLAB Synergy Flow Chemistry
Product line: Small Molecule, Single crystal
Application number Title Body Product name Industries
PX018 An all-in-one software package for single crystal X-ray diffraction CrysAlisPro is the dynamic data collection and data processing program supplied with Rigaku Oxford Diffraction systems. It is designed with an intuitive and user-friendly graphical user interface that runs in fully automatic, semiautomatic or manual modes. At the heart of the program are four modules that take the user through automatic crystal screening, strategy calculation, data collection, and data processing. CrysAlisPro emphasizes live feedback, such as crystal quality and data statistics throughout sample screening and data collection, and guides the user on the best exposure time and image rotation width. Furthermore, CrysAlisPro integrates control of system components, making it possible to run the entire crystallography experiment from one program. CrysAlis Pro Academic research, Pharmaceuticals
SMX004 Twin and multi-crystal experiments Rigaku Oxford Diffraction’s hardware coupled with CrysAlis software makes handling twins easier and produces better results than ever thanks to an improved data reduction algorithm. Best crystallographic practice dictates that all measurable diffraction peaks from a sample should be collected and included in refinement for the most accurate and meticulous structure determination. CrysAlis Pro Academic research, Pharmaceuticals, Chemistry
SMX006 Examining a five-dimensional incommensurate composite crystal structure by X-ray diffraction Modulated structures are a real test of a single crystal diffractometer because of the presence of strong/intense Bragg reflections alongside weaker satellite peaks. Rigaku Oxford Diffraction’s sealed tube systems are an excellent match for conducting research on these materials CrysAlis Pro, XtaLAB Synergy-R, XtaLAB Synergy-S, XtaLAB Synergy-i, XtaLAB Synergy-DW VHF Academic research, Pharmaceuticals, Chemistry, Materials science
SMX010 Stereochemistry of sucrose and a phenidate derivative using copper source of the XtaLAB Synergy-i Due to the approximate λ³ relationship with diffracted intensity, Cu Kα typically provides the strongest signal at the detector and thus enables faster experiments or easier study of small, weakly diffracting samples such metal organic frameworks (MOFs). Due to the stronger anomalous signal obtained from Cu Kα radiation vs. other common wavelengths it is possible to confirm the chirality for lighter atom structures such as purely organic materials with greater accuracy. Additionally, the longer wavelength of Cu Kα radiation can improve peak separation and consequently data quality for cases where reflection overlap is a concern, e.g. twinned crystals or long unit cell axes. XtaLAB Synergy-i Academic research, Pharmaceuticals, Chemistry, Materials science
SMX011 Superior data quality achieved with the XtaLAB Synergy-i, microfocus Mo source Mo Kα radiation is ideal for evaluating large crystal samples, crystals that contain several heavy atoms and crystal samples that are densely packed with heavy atoms. Some examples of such crystals include: minerals, metal clusters or other inorganic materials like perovskites. By studying these sample types using Mo Kα radiation it is possible to reduce absorption effects and achieve better data quality overall. In addition to studying highly absorbing samples it is also possible to obtain high resolution datasets using Mo Kα radiation and perform charge density measurements. Through sophisticated charge density refinements it is possible to determine the bond connectivity and electron placement for a particular crystal structure in more detail. XtaLAB Synergy-i Academic research, Materials science, Chemistry
SMX017 Determining structure of volatile compounds with the crystalline sponge method The crystalline sponge method was applied to gas phase analytes. In many industries, detection and identification of an analyte in the gas phase analytes is the only possibility and typically precludes direct observation of 3D structure. To demonstrate the capabilities of this technique, several odours were captured with crystalline sponges and their structures determined. XtaLAB Synergy-S, HyPix-6000HE Chemistry, Pharmaceuticals, Academic research
SMX018 Structures in Seconds with ‘What Is This?’ Using carefully selected strategies, the ‘What is this?’ tool allows for the fast collection of a minimal dataset solely aimed at providing a structure. Following sample screening the ‘What is this?’ tool becomes available for fast sample identification. The user may choose to continue with a traditional pre-experiment or attempt to identify the structure using ‘What is this?’. The tool requires only an list of elements present in the structure and an exposure time. CrysAlis Pro, XtaLAB Synergy-i, XtaLAB Synergy-R, XtaLAB Synergy-S, XtaLAB mini II Chemistry, Pharmaceuticals, Academic research
SMX019 The HyPix-6000HE detector and its ability to resolve reflections at close crystal-to-detector distances the HyPix-6000HE is able to resolve reflections very well, even at close crystal-to-detector distances, and produce excellent crystal structures in conjunction with the software package, CrysAlis Pro. CrysAlis Pro, XtaLAB Synergy-i, XtaLAB Synergy-R, XtaLAB Synergy-S, HyPix-6000HE Chemistry, Pharmaceuticals, Academic research
SMX023 Charge-Density Data Collection on XtaLab Synergy-S with HyPix 6000 The Rigaku XtaLab Synergy-S is the required fusion of high-end hardware and software, providing new possibilities for experimental charge-density determination. HyPix-6000HE, XtaLAB Synergy-S, CrysAlis Pro Chemistry, Pharmaceuticals, Academic research
SMX024 Charge-Density Data Collection on XtaLab Synergy diffractometers For the correct experimental determination of the charge-density distribution within crystalline structures, reliable high-resolution diffraction data are imperative. The Rigaku XtaLab Synergy series provides the fusion of high-end hard- and software, providing new possibilities for experimental charge- density determination. HyPix-6000HE, XtaLAB Synergy-S, CrysAlis Pro Chemistry, Pharmaceuticals, Academic research
SMX027 Micro Powder Diffraction on XtaLAB Synergy Single Crystal Diffractometers Powder diffraction experiments are traditionally carried out with dedicated powder diffractometers. However, if only micrograms of sample are available, the sample volume is too small to use standard powder diffractometers. The microfocus high-brilliance X-ray sources and high-performance detectors used in Rigaku Oxford Diffraction XtaLAB Synergy systems enable users to collect microdiffraction data without any configuration changes and with data collection times and quality on par with dedicated powder diffractometers. XtaLAB Synergy-S, XtaLAB Synergy-i, XtaLAB Synergy-R Academic research, Pharmaceuticals, Chemistry, Materials science
SMX028 Calibrating the XtaLAB Synergy-S for Pair Distribution (PDF) Analysis Pair Distribution Function (PDF) Analysis1 has become a versatile tool for understanding the structure, and ultimately properties, of materials. Under normal circumstances, PDF is a technique performed using powdered samples and on suitable powder diffractometers. Modern microfocus single crystal diffractometers contain exceptionally bright sources and feature ultralow-noise HPC detectors that make them capable of performing high-quality diffraction experiments on microgram quantities of powder. A natural extension of these features is to perform PDF experiments on such equipment. XtaLAB Synergy-S Academic research, Chemistry, Materials science
SMX029 "What is This?" and Data Collection on Metal-Organic Framework Microcrystals Using the XtaLAB Synergy-S The chemistry of metal-organic framework microcrystals (MOFs) very often produces a crystalline material that is not suitable for standard single crystal diffraction (SCX). Although quality may be improved by recrystallization, sometimes this is not possible, especially when thermal activation processes were used during MOF preparation. A mixture of powder, amorphous material, polycrystalline compounds and microcrystals is a common outcome, which makes MOFs challenging materials both for SCX or PXRD structure determination approaches. XtaLAB Synergy-S Academic research, Chemistry, Materials science
SMX030 Application of the Crystalline Sponge Method for Structure Determination of Persistent Organic Pollutants of Agrochemical Degradation Products The crystalline sponge (CS) method is a novel technique for SCX sample preparation developed by Prof. Fujita,1 which utilizes a crystal of a metal-organic framework (MOF) as a precrystallized molecular container that can incorporate a wide variety of small molecules within the pores and arrange the molecules in a regular pattern according to the periodicity of the host crystal. SCX analysis of the resultant inclusion crystal facilitates direct observation of the molecular structure of the target analyte. Here we report the initial examples of the structure identification of agrochemical metabolites from only a few micrograms of them. We demonstrate that the SCX analysis clearly distinguished the metabolites with very similar structures, which is extremely challenging for a conventional method using nuclear magnetic resonance (NMR) and mass spectrometric (MS) analysis. XtaLAB Synergy-S Academic research, Chemistry, Materials science
SMX033 XtaLAB Synergy-ED: A True Electron Diffractometer Recognizing the potential of MicroED, Rigaku and JEOL announced a collaboration in 2020 to develop a new product designed in a fashion that will make it easy for any crystallographer to use. The resulting product is the XtaLAB Synergy-ED, a new and fully integrated electron diffractometer, that creates a seamless workflow from data collection to structure determination of three-dimensional molecular structures. The XtaLAB Synergy-ED combines core technologies from the two companies: Rigaku’s high-speed, high-sensitivity detector (HyPix-ED), and instrument control and single crystal analysis software platform (CrysAlisPro ED), and JEOL’s expertise in generation and control of stable electron beams. XtaLAB Synergy-ED Academic research, Chemistry, Materials science
SMX034 The "Molecular Grabber" Method: Another Crystalline Sponge Using Protein The CS method utilizes metal-organic frameworks (MOFs) as the pre-crystallized ‘‘container” for the analytes. The “container” is equipped with flexible features to fit various analytes and must have enough space to accommodate a wide variety of molecules. An MOF is a large structural object with three-dimensional networks; thus, the spaces to accommodate molecules have limitations in principle. To overcome the above difficulty, we came up with the idea of a “molecular grabber,” utilizing an easy-to-crystallize protein that has a multi-site binding pocket to bind a variety of types of molecules and gives high-resolution spots. XtaLAB Synergy Custom Academic research, Chemistry, Materials science
SMX035 Stress Evaluation of MLCC Using the XtaLAB Synergy-S Multilayer ceramic capacitors (MLCC) use alternating layers of barium titanate (BaTiO₃, dielectric) and Ni (electrode, Figure 1). Since Ni and BaTiO₃ have different properties, internal stress is generated after firing of MLCC multilayers due to the difference in thermal expansion coefficient between the layers. In recent years, it has become necessary to make the BaTiO₃ layer thinner as the size and capacity increase. Due to the large number of layers and the increased tendency for residual stress, controlling the stress is becoming more and more important. As a result of the continued miniaturization of MLCCs, microdiffraction is becoming a more appropriate method to characterize these multilayers. In this application note, MLCC stress analysis was performed using the XtaLAB Synergy-S, which is a single crystal X-ray diffractometer with a beam size of Ø=100 μm and has a sphere of confusion of 7 μm. XtaLAB Synergy-S Chemistry, Academic research, Electronic parts
SMX036 Comparison of Two XtaLAB Synergy Instruments This application note compares two differently configured XtaLAB Synergy instruments, covering the middle to high range of single crystal diffraction equipment. XtaLAB Synergy-S, XtaLAB Synergy-R, XtaLAB Synergy-DW VHF Academic research, Chemistry, Materials science
SMX037 Identification of a fungicide degradant using the XtaLAB Synergy-ED One such field where crystallization can be an obstacle is determining the stereochemistry of degradation products of biologically active compounds such as fungicides. Electron diffraction can provide three-dimensional structural information on samples as small as a few tens or hundreds of nanometers in thickness. This makes it a valuable tool for cases where the above issues exist. XtaLAB Synergy-ED Academic research, Chemistry, Materials science
SMX039 The Absolute Structure of Light Atom-Containing Molecules In the latest generation of Rigaku’s XtaLAB Synergy systems, the combination of the latest ultrabright microfocus PhotonJet X-ray source technologies, and innovative HyPix detectors, allows us to lower the barrier for absolute structure determination. This application note will showcase two examples: Naproxen, an important API molecule; and Cholestane as an example of a chiral natural product. XtaLAB Synergy-S, XtaLAB Synergy-DW VHF, HyPix-Arc 150° Academic research, Chemistry, Materials science
Product line: Protein, Small Molecule, Single crystal
Application number Title Body Product name Industries
PX027 Synergy of PX and SMX on one diffractometer with the HyPix-Arc 150° Small molecule and macromolecular crystallographers use the same technique, often work in close proximity, and sometimes collaborate on the same projects, yet they are mostly separate in practice, many times even using separate diffractometers in the same room. Our newest diffractometers were designed around the concept of synergy of techniques. Here, we use our newest hybrid photon counting detector, the HyPix-Arc 150°, to demonstrate this synergy. We use the same instrument to collect atomic resolution data sets of lysozyme with and without sucrose bound and of sucrose by itself. We also solve all three structures by experimental phasing. HyPix-Arc 150°, XtaLAB Synergy-R, XtaLAB Synergy-S Academic research
Product line: Single crystal, XRD
Application number Title Body Product name Industries
SMX032 PDF analysis of glassy materials on a home laboratory diffractometer PDF analysis can calculate interatomic distance of heavy elements, which may be effective for calculating the distance between metals in the center of Pc molecules. SmartLab SE, XtaLAB Synergy-R, SmartLab Materials science, Chemistry