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Single crystal X-ray diffraction application notes

Product line: Protein, Single crystal
Application number Title Body Product name Industries
PX0012 Automatic processing of a large synchrotron dataset

 

CrysAlisPro is a comprehensive crystallographic software package for data collection and data reduction on Rigaku Oxford Diffraction single-crystal X-ray diffractometers. With two dedicated user interfaces (CrysAlisPro PX for protein applications and CrysAlisPro SM for small molecule applications), the software is easily optimized for specific experiments. Also, CrysAlisPro is not limited to processing data collected on Rigaku Oxford Diffraction systems. Users can easily import and read data from many external detector formats including CCD, CMOS, hybrid pixel array detector (HPAD) and

CrysAlis Pro Synchrotrons & beamlines, Academic research, Pharmaceuticals
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
PX025 Resolving Reflections from Large Unit Cells at Short Detector Distances Reflections along the long unit cell edge of catalase (~230 Å) were resolved at a short detector distance of 70 mm by using a motorized slit on the XtaLAB Synergy-S to reduce the beam divergence to ~4 mrad. Data from an overnight diffraction experiment were processed to 1.91 Å and used to solve the crystal structure of catalase by molecular replacement. XtaLAB Synergy-S Pharmaceuticals, Academic research
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
Product line: Protein, Single crystal, Optics
Application number Title Body Product name Industries
PX011 VariMax™ optics Based on innovative technologies, Rigaku’s VariMax optics deliver more than double the flux of the previous “King of Flux,” the Confocal Max-Flux® Blue. However, while promised by many optics, increased flux for your protein X-ray system is only part of the story. VariMax Academic research, Pharmaceuticals
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
SMX007 Absolute Structure of L-Alanine Determining the absolute structure of light-atom organic molecules is a developing field with several research groups working on novel statistical methods in data refinement. All of these methods require precise experimental determination of very small differences in the intensities of related reflections. With high intensity sources and ultra-sensitive, low noise detectors coupled with efficient data collection strategies Rigaku Oxford Diffraction’s micro-focus SuperNova X-ray diffractometer is well suited to this field. XtaLAB Synergy-S, XtaLAB Synergy-R, XtaLAB Synergy-i Chemistry, Academic research, Pharmaceuticals
SMX009 Efficient data coverage using a kappa goniometer Rigaku Oxford Diffraction recently launched the XtaLAB Synergy systems, which amongst many improvements, includes an updated goniometer. The goniometer incorporates the following features: new motors allowing it to move twice as fast as its predecessor and with very high accuracy, a symmetrical theta range for flexibility in gathering data in reciprocal space, a new beamstop holder design to allow the detector to be positioned nearer to the sample and a telescoping theta arm for long detector distances. XtaLAB Synergy-DW VHF, XtaLAB Synergy-i, XtaLAB Synergy-R, XtaLAB Synergy-S Chemistry, Academic research, Pharmaceuticals, 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
SMX013 Improving data quality for a highly absorbing mineral, Hereroite, with the PhotonJet Ag source When collecting X-ray data on samples containing several heavy elements that are densely packed, for example; minerals, crystalline alloys, metal clusters and other inorganic materials such as perovskites, absorption can be an issue. The total absorption (μ) of any sample is dependent on the sample composition, packed sample density, the size of the crystal, and the X-ray wavelength. By reducing the latter you can lower the overall absorption and get improved data quality. For home-lab instruments considerable benefits can be found for these types of samples by employing silver radiation which has a shorter wavelength (0.56 Å). XtaLAB Synergy-S Academic research, Chemistry, Materials science
SMX014 Higher flux from XtaLAB Synergy-DW leads to improved data for small crystals and challenging samples Single crystal X-ray diffraction is the preferred method for structure determination of small molecules as well as protein and larger biological macromolecules. The complexity of samples that can be studied using X-ray techniques has improved significantly over recent years. Samples that were previously too small to be considered for single crystal X-ray analysis are now fully amenable to study. Highly unstable and weakly diffracting samples may be studied immediately, samples do not need to be discarded or undergo further recrystallization attempts. XtaLAB Synergy-DW VHF Chemistry, Pharmaceuticals, Academic research
SMX015 The Universal Goniometer: Complete Data Sets on All Crystals, No Compromise A small crystal of chlorothiazide, with dimensions 0.019 x 0.035 x 0.046 mm, was captured within a thin layer of paratone oil inside a fiber loop mounted on a magnetic base. The crystal was mounted on the Universal Goniometer of a microfocus sealed tube XtaLAB Synergy-S X-ray diffractometer and data were collected at 100 K using ROD software, CrysAlis(Pro). XtaLAB Synergy-DW VHF, XtaLAB Synergy-R, XtaLAB Synergy-S Chemistry, Pharmaceuticals, Academic research
SMX016 Analysis of Very Small Organic Crystals with the XtaLAB Synergy-S A very small crystal of benzophenone, with dimensions 0.015 x 0.018 x 0.027 mm³, was captured on a MiTeGen Kapton loop mounted on a magnetic base, using paratone oil. The crystal was mounted on the goniometer, centered in the beam using a video camera and data were collected at 100 K with the Rigaku Oxford Diffraction program CrysAlis(Pro). XtaLAB Synergy-S, HyPix-6000HE Chemistry, Pharmaceuticals, Academic research
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
SMX020 HyPix-6000HE HPC detector vs. Eos S2 CCD Data processing was carried out in order to achieve the best result for each detector in terms of the final R1 and Flack parameter determination. The results are shown in this report. CrysAlis Pro, XtaLAB Synergy-i, XtaLAB Synergy-R, XtaLAB Synergy-S, HyPix-6000HE Chemistry, Pharmaceuticals, Academic research
SMX021 Fast crystallography on a difficult sample The new XtaLAB Synergy-R diffractometer with HyPix-6000HE hybrid photon counting (HPC) detector is designed specifically for the most challenging of small molecule samples. XtaLAB Synergy-R, HyPix-6000HE, CrysAlis Pro Chemistry, Pharmaceuticals, Academic research
SMX022 Data quality improvements using the XtaLAB Synergy The new XtaLAB Synergy diffractometer represents improvements in both hardware and software design. Advancements have been made not only in the microfocus sources but also in the goniometer hardware. XtaLAB Synergy-R, XtaLAB Synergy-S, CrysAlis Pro 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
SMX025 The Crystalline Sponge Method on XtaLAB Synergy Systems The Crystalline Sponge (CS) method is an approach to obtain single-crystal X-ray structures of compounds, that are difficult or impossible to crystallize, for example because they are of too small a quantity, are not solid at ambient conditions or form amorphous precipitates. In some cases spectroscopic or spectrometric techniques cannot give definitive answers to the analytical problems so a crystal structure is needed. CrysAlis Pro, XtaLAB Synergy-i, XtaLAB Synergy-R, XtaLAB Synergy-S, HyPix-6000HE Chemistry, Pharmaceuticals, Academic research
SMX026 High-Pressure Data Collection on the XtaLAB Synergy-S with Ag radiation and Using CrysAlis Pro X-ray sources using Ag Kα radiation offer a shorter wavelength (0.56 Å) than the traditional Cu (1.54 Å) or Mo (0.71 Å) sources found in most home laboratory instruments. Shorter-wavelength, higher-energy X-rays, often called ‘hard’ X-rays, are generally absorbed to a lesser extent by samples, but also diffract with smaller angles such that there are more measurable reflections within a given theta angle when compared to long wavelengths. This can be exploited in a number of different ways. For samples containing heavy elements, absorption artefacts are minimized. For charge density measurements, more reflections are observed to higher resolution. For high-pressure measurements there are fewer inaccessible reflections as a result of the restrictive pressure cell. XtaLAB Synergy-S, CrysAlis Pro Materials science, Academic research, Chemistry
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
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