Diffraction Data Collection Research Articles

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures.

Neutron crystallography is a structural technique that allows determination of hydrogen atom positions within biological macromolecules, yielding mechanistically important information about protonation and hydration states while not inducing radiation damage. X-ray diffraction, in contrast, provides only limited information on the position of light atoms and the X-ray beamrapidly induces radiation damage of photosensitivecofactors and metal centers. Presented here is the workflow employed for the IMAGINE and MaNDi beamlines at Oak Ridge National Laboratory (ORNL) to obtain a neutron diffraction structure once a protein crystal of suitable size (> 0.1 mm3) has been grown. We demonstrate mounting of hydrogenated proteincrystals in quartz capillaries for neutron diffraction data collection. Also presented is the vapor exchange process of the mounted crystals with D2O-containing buffer to ensure replacement of hydrogen atoms at exchangeable sites with deuterium. The incorporation of deuterium reduces the background arising from the incoherent scattering of hydrogen atoms and prevents density cancellation caused by their negative coherent scattering length. Sample alignment and room temperature data collection strategies are illustrated using quasi-Laue data collection at IMAGINE at the High Flux Isotope Reactor (HFIR). Furthermore, crystal mounting and rapid freezing in liquid nitrogen for cryo-data collection to trap labile reaction intermediates is demonstrated at the MaNDi time-of-flight instrument at the Spallation Neutron Source (SNS). Preparation of the model coordinate and diffraction data files and visualization of the neutron scattering length density (SLD) maps will also be addressed. Structure refinement against neutron data-only or against joint X-ray/neutron data to obtain an all-atom structure of the protein of interest will finally be discussed. The process of determining a neutron structure will be demonstrated using crystals of the lytic polysaccharide monooxygenase Neurospora crassa LPMO9D, a copper-containing metalloprotein involved in the degradation of recalcitrant polysaccharides via oxidative cleavage of the glycosidic bond.

Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures.

Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293-363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.

Protein-crystal detection with a compact multimodal multiphoton microscope

There is an increasing demand for rapid, effective methods to identify and detect protein micro- and nano-crystal suspensions for serial diffraction data collection at X-ray free-electron lasers or high-intensity micro-focus synchrotron radiation sources. Here, we demonstrate a compact multimodal, multiphoton microscope, driven by a fiber-based ultrafast laser, enabling excitation wavelengths at 775 nm and 1300 nm for nonlinear optical imaging, which simultaneously records second-harmonic generation, third-harmonic generation and three-photon excited ultraviolet fluorescence to identify and detect protein crystals with high sensitivity. The instrument serves as a valuable and important tool supporting sample scoring and sample optimization in biomolecular crystallography, which we hope will increase the capabilities and productivity of serial diffraction data collection in the future.

Stable and Highly Flexible Perovskite Solar Cells with Power Conversion Efficiency Approaching 20% by Elastic Grain Boundary Encapsulation

Here, we show that flexible perovskite solar cells (PSCs) with high operational stability and power conversion efficiency (PCE) approaching 20% were achieved by elastic grain boundary (GB) encapsul...

Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase.

A membrane-bound hydrogenase from Desulfovibrio vulgaris Miyazaki F is a metalloenzyme that contains a binuclear Ni-Fe complex in its active site and mainly catalyzes the oxidation of molecular hydrogen to generate a proton gradient in the bacterium. The active-site Ni-Fe complex of the aerobically purified enzyme shows its inactive oxidized form, which can be reactivated through reduction by hydrogen. Here, in order to understand how the oxidized form is reactivated by hydrogen and further to directly evaluate the bridging of a hydride ligand in the reduced form of the Ni-Fe complex, a neutron structure determination was undertaken on single crystals grown in a hydrogen atmosphere. Cryogenic crystallography is being introduced into the neutron diffraction research field as it enables the trapping of short-lived intermediates and the collection of diffraction data to higher resolution. To optimize the cooling of large crystals under anaerobic conditions, the effects on crystal quality were evaluated by X-rays using two typical methods, the use of a cold nitrogen-gas stream and plunge-cooling into liquid nitrogen, and the former was found to be more effective in cooling the crystals uniformly than the latter. Neutron diffraction data for the reactivated enzyme were collected at the Japan Photon Accelerator Research Complex under cryogenic conditions, where the crystal diffracted to a resolution of 2.0 Å. A neutron diffraction experiment on the reduced form was carried out at Oak Ridge National Laboratory under cryogenic conditions and showed diffraction peaks to a resolution of 2.4 Å.

Microplates for Crystal Growth and in situ Data Collection at a Synchrotron Beamline

An efficient data collection method is important for microcrystals, because microcrystals are sensitive to radiation damage. Moreover, microcrystals are difficult to harvest and locate owing to refraction effects from the surface of the liquid drop or optically invisible, owing to their small size. Collecting X-ray diffraction data directly from the crystallization devices to completely eliminate the crystal harvesting step is of particular interest. To address these needs, novel microplates combining crystal growth and data collection have been designed for efficient in situ data collection and fully tested at Shanghai Synchrotron Radiation Facility (SSRF) crystallography beamlines. The design of the novel microplates fully adapts the advantage of in situ technology. Thin Kapton membranes were selected to seal the microplate for crystal growth, the crystallization plates can support hanging drop and setting drop vapor diffusion crystallization experiments. Then, the microplate was fixed on a magnetic base and mounted on the goniometer head for in situ data collection. Automatic grid scanning was applied for crystal location with a Blu-Ice data collection system and then in situ data collection was performed. The microcrystals of lysozyme were selected as the testing samples for diffraction data collection using the novel microplates. The results show that this method can achieve comparable data quality to that of the traditional method using the nylon loop. In addition, our method can efficiently and diversely perform data acquisition experiments, and be especially suitable for solving structures of multiple crystals at room temperature or cryogenic temperature.

Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips.

Sample handling and manipulation for cryoprotection currently remain critical factors in X-ray structural determination. While several microchips for macromolecular crystallization have been proposed during the last two decades to partially overcome crystal-manipulation issues, increased background noise originating from the scattering of chip-fabrication materials has so far limited the attainable resolution of diffraction data. Here, the conception and use of low-cost, X-ray-transparent microchips for in situ crystallization and direct data collection, and structure determination at atomic resolution close to 1.0 Å, is presented. The chips are fabricated by a combination of either OSTEMER and Kapton or OSTEMER and Mylar materials for the implementation of counter-diffusion crystallization experiments. Both materials produce a sufficiently low scattering background to permit atomic resolution diffraction data collection at room temperature and the generation of 3D structural models of the tested model proteins lysozyme, thaumatin and glucose isomerase. Although the high symmetry of the three model protein crystals produced almost complete data sets at high resolution, the potential of in-line data merging and scaling of the multiple crystals grown along the microfluidic channels is also presented and discussed.

The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions.

Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.

Assessing Rietveld refinement results on silicon carbide nanoparticles produced by magnesiothermal treatment

Collection and evaluation of X-ray diffraction (XRD) data are essential not purely for phase and structural investigation, but more importantly for all intends and purposes of comprehensive materials characterizations. Incorrect XRD analysis result will lead to misinterpretation of the phase and structural characteristics. The worst part is that instigates inappropriate interpretation of other phase-dependent or structural-dependent properties, e.g. electric, magnetic, or thermodynamic properties. Consequently, accurate phase identification and crystal structure quantification from XRD data is inevitable prior to further materials characterizations, most significantly for nanomaterials. In this present study, we reported the complete XRD qualitative and quantitative analyses of silicon carbide (SiC) nanoparticles. The phase identification was run using X’Pert High Score Plus (HSP) software. Furthermore, the crystal structure computation was executed by means of different Rietveld-based computer programs, i.e. HSP, MAUD (Material Analysis using Diffraction), GSAS (General Structure Analysis System) and Rietica. Our research revealed that the synthesized silicon carbide preserved a cubic crystal structure. MAUD and GSAS could predict the equivalent particle size which was close to that of captured by transmission electron microscopy (TEM). In addition, MAUD produced the most accurate value of the particle size. In this case, Rietica and MAUD extracted similar lattice parameter of the silicon carbide. At last but not least, the electron density mapping also presented to confirm the cubic crystal structure formation of the silicon carbide nanoparticles.

Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron.

The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.

ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam.

ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 1013 photons s-1), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.

3D-printed holders for in meso in situ fixed-target serial X-ray crystallography.

The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.

Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography.

Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.

Gold(I), silver(I) and copper(I) complexes of 2,4,6-trimethylphenyl-3-benzoylthiourea; synthesis and biological applications

2,4,6-Trimethylphenyl-3-benzoylthiourea (L) and its gold(I), silver(I) and copper(I) complexes were synthesized. Treatment of L with HAuCl4, AgNO3 and CuI in CH3CN afforded complexes of general representation, M(L)X, where M/X = Au/Cl (1), Ag/NO3 (2), Cu/I (3). Reaction with Au3+ salt afforded two products, wherein complex containing Au+ (reduced under normal and aerobic reaction conditions ca. 66% on NMR time scale) was confirmed by X-ray diffraction for a single crystal of complex 1. The minor fraction (ca. 33%, from 1H NMR data) in the reaction mixture was identified as complex 4 with a general formula [AuL2]Cl3. Reaction with AgNO3 and CuI exclusively afforded pure products 2 and 3. Ligand L and complexes 1–4 were characterized by UV/visible, FT-IR and 1H-, 13C NMR spectroscopy. Complex 1 is crystalline in nature and good quality crystals were obtained which allowed for collection of diffraction data and the structure was thus confirmed. Solution state and solid state structures have been compared. The resultant complexes were tested for their cytotoxicity, antibacterial, antifungal, antioxidant and DNA binding activities. Complex 1 (Au based) showed promising activities in comparison with the available selected drugs used as standards.

Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines.

Reducing the sample-exchange time is a crucial issue in maximizing the throughput of macromolecular crystallography (MX) beamlines because the diffraction data collection itself is completed within a minute in the era of pixel-array detectors. To this end, an upgraded sample changer, SPACE-II, has been developed on the basis of the previous model, SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), at the BL41XU beamline at SPring-8. SPACE-II achieves one sample-exchange step within 16 s, of which its action accounts for only 11 s, because of three features: (i) the implementation of twin arms that enable samples to be exchanged in one cycle of mount-arm action, (ii) the implementation of long-stroke mount arms that allow samples to be exchanged without withdrawal of the detector and (iii) the use of a fast-moving translation and rotation stage for the mount arms. By pre-holding the next sample prior to the sample-exchange sequence, the time was further decreased to 11 s in the case of automatic data collection, of which the action of SPACE-II accounted for 8 s. Moreover, the sample capacity was expanded from four to eight Uni-Pucks. The performance of SPACE-II has been demonstrated in over two years of operation at BL41XU; the average number of samples mounted on the diffractometer in one day was increased from 132 to 185, with an error rate of 0.089%, which counted incidents in which users could not continue with an experiment without recovery work by entering the experimental hutch. On the basis of these results, SPACE-II has been installed at three other MX beamlines at SPring-8 as of July 2019. The fast and highly reliable SPACE-II is now one of the most important pieces of infrastructure for the MX beamlines at SPring-8, providing users with the opportunity to fully make use of limited beamtime with brilliant X-rays.

The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody

The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody

In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source.

The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.

The macromolecular neutron diffractometer at the spallation neutron source.

The Macromolecular Neutron Diffractometer known as MaNDi is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. Neutrons are produced in discrete pulses at the Spallation Neutron Source, which enables Laue diffraction data through measuring the time-of-flight and thus wavelength of each diffracted neutron. The MaNDi diffractometer is optimized to collect diffraction data from protein crystals with unit cell axes between 30 and 300Å. The instrument is designed to provide flexibility in several instrumental parameters such as wavelength bandwidth and beam divergence to allow data collection from a range systems. Data collection is possible at room temperature or 100K using a standard nitrogen gas stream cooler combined with standard X-ray style mounting pins and loops.

Heme peroxidase-Trapping intermediates by cryo neutron crystallography.

By combining the normal practice for X-ray crystallography of collecting diffraction data at 100K with neutron crystallography the structures of cryo-trapped enzyme intermediates have been determined, revealing the positions of the previously hidden hydrogens that are essential to a better understanding of the involved mechanism.

Depicting the crystal structure of fibrous ferrierite from British Columbia using a combined synchrotron techniques approach.

The ferrierite crystal structure has often been subject to discussion because of the possible lowering of symmetry from the space group Immm. It mainly occurs in nature with a fibrous crystal habit, and because of the existence of line/planar defects in the framework, texture and preferred orientation effects it has been difficult to obtain an exact crystallographic model based only on the results from powder diffraction data. Therefore, nano-single-crystal diffraction and tomography data have been combined in order to improve the refinement with a meaningful model. High-quality single-crystal data, providing reliable structural information, and tomography images have been used as input for a Rietveld refinement which took into account a phenomenological description of stacking disorder and the analytical description of the preferred orientation, by means of spherical harmonics for strong texture effects. This is one of the first examples of application of synchrotron nano-diffraction for the structure solution of fibrous minerals of micrometre to nanometre size. The high quality of the crystals allowed collection of single-crystal X-ray diffraction data of up to 0.6 Å resolution, leading to an unambiguous solution and precise anisotropic refinement. Nano-single-crystal diffraction and phase contrast tomography data were collected at ID11 and the high-resolution powder diffraction patterns at ID22 of the European Synchrotron Radiation Facility. This detailed crystallographic characterization provides a basis for understanding the potential of ferrierite for toxicity and carcinogenicity.