scholarly journals Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography

2016 ◽  
Vol 72 (8) ◽  
pp. 944-955 ◽  
Author(s):  
Saeed Oghbaey ◽  
Antoine Sarracini ◽  
Helen M. Ginn ◽  
Olivier Pare-Labrosse ◽  
Anling Kuo ◽  
...  
Keyword(s):  
Atmospheric Pressure ◽  
Spectral Mapping ◽  
Fixed Target ◽  
X Ray ◽  
Experimental Scheme ◽  
Novel Structure ◽  
Laser Sources ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography

The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means ofin situspectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.

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

2020 ◽  
Vol 53 (3) ◽  
pp. 854-859
Author(s):  
Chia-Ying Huang ◽  
Nathalie Meier ◽  
Martin Caffrey ◽  
Meitian Wang ◽  
Vincent Olieric
Keyword(s):  
Data Collection ◽  
Heavy Atom ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sample Stability ◽  
3D Printed ◽  
Sponge Phase ◽  
Serial 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.

scholarly journals The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation

2019 ◽  
Vol 26 (3) ◽  
pp. 660-676 ◽  
Author(s):  
Adrian P. Mancuso ◽  
Andrew Aquila ◽  
Lewis Batchelor ◽  
Richard J. Bean ◽  
Johan Bielecki ◽  
...  
Keyword(s):  
Structure Determination ◽  
High Repetition Rate ◽  
Optical Systems ◽  
Diagnostic Tools ◽  
Imaging Method ◽  
Single Particles ◽  
X Ray ◽  
Data Rates ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation – in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.

Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Deepshika Gilbile ◽  
Megan L. Shelby ◽  
Artem Y. Lyubimov ◽  
Jennifer L. Wierman ◽  
Diana C. F. Monteiro ◽  
...  
Keyword(s):  
Room Temperature ◽  
Microfluidic Chips ◽  
Fixed Target ◽  
Plug And Play ◽  
X Ray ◽  
X Ray Crystallography ◽  
Serial Crystallography

This work presents our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial X-ray crystallography measurements.

scholarly journals Nanoclay Intercalation During Foaming of Polymeric Nanocomposites Studied in-Situ by Synchrotron X-Ray Diffraction

Materials ◽  
2018 ◽  
Vol 11 (12) ◽  
pp. 2459
Author(s):  
Victoria Bernardo ◽  
Mikel Mugica ◽  
Saul Perez-Tamarit ◽  
Belen Notario ◽  
Catalina Jimenez ◽  
...  
Keyword(s):  
Atmospheric Pressure ◽  
Catalytic Effect ◽  
Decomposition Temperature ◽  
Melt Blending ◽  
Polymeric Nanocomposites ◽  
X Ray Diffraction ◽  
X Ray ◽  
Foaming Process ◽  
Key Parameter

The intercalation degree of nanoclays in polymeric foamed nanocomposites containing clays is a key parameter determining the final properties of the material, but how intercalation occurs is not fully understood. In this work, energy dispersive X-ray diffraction (ED-XRD) of synchrotron radiation was used as an in-situ technique to deepen into the intercalation process of polymer/nanoclay nanocomposites during foaming. Foamable nanocomposites were prepared by the melt blending route using low-density polyethylene (LDPE), polypropylene (PP), and polystyrene (PS) with surface treated nanoclays and azodicarbonamide (ADC) as the blowing agent. Foaming was induced by heating at atmospheric pressure. The time and temperature evolution of the interlamellar distance of the clay platelets in the expanding nanocomposites was followed. Upon foaming, interlamellar distances of the nanocomposites based on LDPE and PP increase by 18% and 16% compared to the bulk foamable nanocomposite. Therefore, the foaming process enhances the nanoclay intercalation degree in these systems. This effect is not strongly affected by the type of nanoclay used in LDPE, but by the type of polymer used. Besides, the addition of nanoclays to PP and PS has a catalytic effect on the decomposition of ADC, i.e., the decomposition temperature is reduced, and the amount of gas released increases. This effect was previously proved for LDPE.

scholarly journals Dehydrogenation of Ethylene on Supported Palladium Nanoparticles: A Double View from Metal and Hydrocarbon Sides

Nanomaterials ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1643 ◽  
Author(s):  
Oleg A. Usoltsev ◽  
Anna Yu. Pnevskaya ◽  
Elizaveta G. Kamyshova ◽  
Andrei A. Tereshchenko ◽  
Alina A. Skorynina ◽  
...  
Keyword(s):  
Atmospheric Pressure ◽  
Palladium Nanoparticles ◽  
Pd Catalyst ◽  
X Ray Diffraction ◽  
Reaction Conditions ◽  
X Ray ◽  
Ab Initio Simulations ◽  
Supported Palladium ◽  
X Ray Absorption

Adsorption of ethylene on palladium, a key step in various catalytic reactions, may result in a variety of surface-adsorbed species and formation of palladium carbides, especially under industrially relevant pressures and temperatures. Therefore, the application of both surface and bulk sensitive techniques under reaction conditions is important for a comprehensive understanding of ethylene interaction with Pd-catalyst. In this work, we apply in situ X-ray absorption spectroscopy, X-ray diffraction and infrared spectroscopy to follow the evolution of the bulk and surface structure of an industrial catalysts consisting of 2.6 nm supported palladium nanoparticles upon exposure to ethylene under atmospheric pressure at 50 °C. Experimental results were complemented by ab initio simulations of atomic structure, X-ray absorption spectra and vibrational spectra. The adsorbed ethylene was shown to dehydrogenate to C2H3, C2H2 and C2H species, and to finally decompose to palladium carbide. Thus, this study reveals the evolution pathway of ethylene on industrial Pd-catalyst under atmospheric pressure at moderate temperatures, and provides a conceptual framework for the experimental and theoretical investigation of palladium-based systems, in which both surface and bulk structures exhibit a dynamic nature under reaction conditions.

scholarly journals Serial crystallography using automated drop dispensing

2021 ◽  
Vol 28 (5) ◽  
Author(s):  
Zhen Su ◽  
Joshua Cantlon ◽  
Lacey Douthit ◽  
Max Wiedorn ◽  
Sébastien Boutet ◽  
...  
Keyword(s):  
Free Electron Laser ◽  
Protein Crystal ◽  
Cross Contamination ◽  
X Ray ◽  
On Demand ◽  
Drop On Demand ◽  
Serial Crystallography ◽  
Cycling System ◽  
Serial Femtosecond Crystallography

Automated, pulsed liquid-phase sample delivery has the potential to greatly improve the efficiency of both sample and photon use at pulsed X-ray facilities. In this work, an automated drop on demand (DOD) system that accelerates sample exchange for serial femtosecond crystallography (SFX) is demonstrated. Four different protein crystal slurries were tested, and this technique is further improved here with an automatic sample-cycling system whose effectiveness was verified by the indexing results. Here, high-throughput SFX screening is shown to be possible at free-electron laser facilities with very low risk of cross contamination and minimal downtime. The development of this technique will significantly reduce sample consumption and enable structure determination of proteins that are difficult to crystallize in large quantities. This work also lays the foundation for automating sample delivery.

scholarly journals Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography

2020 ◽  
Author(s):  
M. Wilamowski ◽  
D.A. Sherrell ◽  
G. Minasov ◽  
Y. Kim ◽  
L. Shuvalova ◽  
...  
Keyword(s):  
Fixed Target ◽  
Innate Response ◽  
Methyltransferase Activity ◽  
X Ray ◽  
Biologically Relevant ◽  
Methylation Reaction ◽  
Before And After ◽  
Serial Crystallography ◽  
Rna Maturation ◽  
First Time

ABSTRACTThe genome of the SARS-CoV-2 coronavirus contains 29 proteins, of which 15 are nonstructural. Nsp10 and Nsp16 form a complex responsible for the capping of mRNA at the 5′ terminus. In the methylation reaction the S-adenosyl-L-methionine serves as the donor of the methyl group that is transferred to Cap-0 at the first transcribed nucleotide to create Cap-1. The presence of Cap-1 makes viral RNAs mimic the host transcripts and prevents their degradation. To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We determined crystal structures of Nsp10/16 that revealed the states before and after the methylation reaction, for the first time illustrating coronavirus Nsp10/16 complexes with the m7GpppAm2′-O Cap-1, where 2′OH of ribose is methylated. We compare these structures with structures of Nsp10/16 at 297 K and 100 K collected from a single crystal. This data provide important mechanistic insight and can be used to design small molecules that inhibit viral RNA maturation making SARS-CoV-2 sensitive to host innate response.

Application of X-Ray Scattering to the in Situ Study of Organometallic Vapor Phase Epitaxy

1988 ◽  
Vol 131 ◽  
Author(s):  
P. H. Fuoss ◽  
D. W. Kisker ◽  
S. Brennan ◽  
J. L. Kahn
Keyword(s):  
Vapor Phase ◽  
Atmospheric Pressure ◽  
Chemical Vapor ◽  
High Signal ◽  
X Ray ◽  
Surface Sensitivity ◽  
X Ray Scattering ◽  
Detailed Surface ◽  
Ray Scattering

ABSTRACTDespite their importance, the detailed surface reactions and rearrangements which occur during chemical vapor deposition remain largely undetermined because of the lack of suitable experimental probes. In principle, x-ray scattering and spectroscopy techniques are well suited to studying these near atmospheric pressure processes but advances in this area have been limited both by the lack of suitable x-ray sources and by the difficulty of integrating the growth and measurement experiments. We have developed equipment and techniques to perform in situ x-ray scattering studies of the structure of surfaces during organometallic vapor phase epitaxial (OMVPE) growth using the extremely bright undulator radiation from the PEP electron storage ring. In this paper, we describe our initial experimental results studying cleaning and subsequent reconstruction of GaAs (001) surfaces in a flowing H2 ambient. These results demonstrate the excellent surface sensitivity, low background and high signal levels necessary to study the dynamic processes associated with semiconductor growth using OMVPE.

scholarly journals CrystFEL: a software suite for snapshot serial crystallography

2012 ◽  
Vol 45 (2) ◽  
pp. 335-341 ◽  
Author(s):  
Thomas A. White ◽  
Richard A. Kirian ◽  
Andrew V. Martin ◽  
Andrew Aquila ◽  
Karol Nass ◽  
...  
Keyword(s):  
Structural Information ◽  
Software Suite ◽  
X Ray ◽  
Large Numbers ◽  
Small Crystals ◽  
Serial Crystallography ◽  
Diffraction Patterns ◽  
Complicated Geometries ◽  
Serial Femtosecond Crystallography

In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.

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