scholarly journals Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

2013 ◽  
Vol 69 (7) ◽  
pp. 1252-1259 ◽  
Author(s):  
Anna J. Warren ◽  
Wes Armour ◽  
Danny Axford ◽  
Mark Basham ◽  
Thomas Connolley ◽  
...  
Keyword(s):  
Decision Making ◽  
Data Collection ◽  
Cubic Phase ◽  
Informed Decision Making ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Shape Estimation ◽  
X Ray ◽  
Raster Scanning ◽  
X Ray Imaging

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

scholarly journals Visualisation of membrane protein crystals using X-ray imaging

2014 ◽  
Vol 70 (a1) ◽  
pp. C351-C351
Author(s):  
Anna Warren ◽  
Wes Armour ◽  
Danny Axford ◽  
Mark Basham ◽  
Thomas Connolley ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Cubic Phase ◽  
Informed Decision Making ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Shape Estimation ◽  
X Ray ◽  
Raster Scanning ◽  
X Ray Imaging

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallise on much smaller scales and are frequently mounted in opaque or highly refractive materials.[1,2] It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this poster the use of X-ray microradiography and microtomography is reported as a tool for crystal visualisation, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals, and crystals mounted in opaque materials such as lipidic cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to a diffraction grid scan. However, for sample location and shape estimation alone, just a few radiographic projections may be required; hence reducing the dose the crystals will be exposed to prior to the diffraction data collection.[3]

scholarly journals Visualization of protein crystals by high-energy phase-contrast X-ray imaging

2019 ◽  
Vol 75 (11) ◽  
pp. 947-958 ◽  
Author(s):  
Maxim Polikarpov ◽  
Gleb Bourenkov ◽  
Irina Snigireva ◽  
Anatoly Snigirev ◽  
Sophie Zimmermann ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Phase Contrast ◽  
High Energy ◽  
Protein Crystals ◽  
Cubic Phase ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Imaging

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallography beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

scholarly journals Automated harvesting and processing of protein crystals through laser photoablation

2016 ◽  
Vol 72 (4) ◽  
pp. 454-466 ◽  
Author(s):  
Ulrich Zander ◽  
Guillaume Hoffmann ◽  
Irina Cornaciu ◽  
Jean-Pierre Marquette ◽  
Gergely Papp ◽  
...  
Keyword(s):  
Data Collection ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Methods ◽  
Repeated Sample ◽  
Sample Recovery ◽  
Through Diffusion ◽  
X Ray Background ◽  
Low X

Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.

RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography

2013 ◽  
Vol 46 (4) ◽  
pp. 1225-1230 ◽  
Author(s):  
Oliver B. Zeldin ◽  
Markus Gerstel ◽  
Elspeth F. Garman
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Diffraction Experiment ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Online Methods ◽  
Crystal Volume ◽  
Number Of Iterations

RADDOSE-3D allows the macroscopic modelling of an X-ray diffraction experiment for the purpose of better predicting radiation-damage progression. The distribution of dose within the crystal volume is calculated for a number of iterations in small angular steps across one or more data collection wedges, providing a time-resolved picture of the dose state of the crystal. The code is highly modular so that future contributions from the community can be easily integrated into it, in particular to incorporate online methods for determining the shape of macromolecular crystals and better protocols for imaging real experimental X-ray beam profiles.

scholarly journals Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography

IUCrJ ◽  
2020 ◽  
Vol 7 (6) ◽  
pp. 1131-1141
Author(s):  
Isabelle Martiel ◽  
Chia-Ying Huang ◽  
Pablo Villanueva-Perez ◽  
Ezequiel Panepucci ◽  
Shibom Basu ◽  
...  
Keyword(s):  
Data Collection ◽  
Phase Contrast ◽  
Low Dose ◽  
Phase Contrast Imaging ◽  
Cubic Phase ◽  
Macromolecular Crystallography ◽  
Contrast Imaging ◽  
X Ray ◽  
Serial Data

Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.

scholarly journals The State of the Canadian Macromolecular Crystallography Facility

2014 ◽  
Vol 70 (a1) ◽  
pp. C1735-C1735
Author(s):  
James Gorin ◽  
Shaunivan Labiuk ◽  
Julien Cotelesage ◽  
Kathryn Janzen ◽  
Michel Fodje ◽  
...  
Keyword(s):  
Data Collection ◽  
Light Source ◽  
Structure Determination ◽  
Low Energy ◽  
Air Bearing ◽  
Beam Size ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Data Management Software

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source consists of two macromolecular crystallography beamlines for structure determination using x-ray diffraction. The equipment at the CMCF beamlines have undergone or will undergo changes and improvements to better meet the needs of the most challenging experiments users may present. Among these improvements are: 1) Automounter improvements; 2) Better goniometry on 08ID-1 with the addition of a Huber air-bearing goniometer; 3) Added beam size capabilities on 08ID-1 with the addition of a multiple beam defining aperture holder; 4) XAFS capability on 08B1-1; 5) Improved low energy S-SAD data collection with the addition of a Helium path; 6) Improvements to the data collection and data management software; 7) A vacuum path for scattering experiments with detector distances up to 1 m; 8) A comprehensive beamline upgrade project on the 08ID-1 beamline; and 9) Service crystallography services.

scholarly journals Dynamic X-ray diffraction sampling for protein crystal positioning

2017 ◽  
Vol 24 (1) ◽  
pp. 188-195 ◽  
Author(s):  
Nicole M. Scarborough ◽  
G. M. Dilshan P. Godaliyadda ◽  
Dong Hye Ye ◽  
David J. Kissick ◽  
Shijie Zhang ◽  
...  
Keyword(s):  
Image Reconstruction ◽  
Data Collection ◽  
Argonne National Laboratory ◽  
Ground Truth ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
X Ray ◽  
Raster Scanning ◽  
Dynamic Sampling ◽  
The Impact

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.

scholarly journals X-ray imaging of silicon die within fully packaged semiconductor devices

2021 ◽  
pp. 1-7
Author(s):  
Brian K. Tanner ◽  
Patrick J. McNally ◽  
Andreas N. Danilewsky
Keyword(s):  
Synchrotron Radiation ◽  
Feasibility Studies ◽  
Monochromatic Radiation ◽  
X Ray Diffraction ◽  
Divergent Beam ◽  
X Ray ◽  
X Ray Imaging ◽  
Setting Process ◽  
Diffraction Imaging ◽  
Lattice Planes

X-ray diffraction imaging (XRDI) (topography) measurements of silicon die warpage within fully packaged commercial quad-flat no-lead devices are described. Using synchrotron radiation, it has been shown that the tilt of the lattice planes in the Analog Devices AD9253 die initially falls, but after 100 °C, it rises again. The twist across the die wafer falls linearly with an increase in temperature. At 200 °C, the tilt varies approximately linearly with position, that is, displacement varies quadratically along the die. The warpage is approximately reversible on cooling, suggesting that it has a simple paraboloidal form prior to encapsulation; the complex tilt and twisting result from the polymer setting process. Feasibility studies are reported, which demonstrate that a divergent beam and quasi-monochromatic radiation from a sealed X-ray tube can be used to perform warpage measurements by XRDI in the laboratory. Existing tools have limitations because of the geometry of the X-ray optics, resulting in applicability only to simple warpage structures. The necessary modifications required for use in situations of complex warpage, for example, in multiple die interconnected packages are specified.

scholarly journals Transport and Dielectric Properties of Mechanosynthesized La2/3Cu3Ti4O12 Ceramics

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 313
Author(s):  
Mohamad M. Ahmad ◽  
Hicham Mahfoz Kotb ◽  
Celin Joseph ◽  
Shalendra Kumar ◽  
Adil Alshoaibi
Keyword(s):  
Dielectric Constant ◽  
Sintering Temperature ◽  
Cubic Phase ◽  
X Ray Diffraction ◽  
Boundary Conductivity ◽  
X Ray ◽  
Giant Dielectric ◽  
Mechanochemical Milling ◽  
Giant Dielectric Constant ◽  
Lower Temperature

La2/3Cu3Ti4O12 (LCTO) powder has been synthesized by the mechanochemical milling technique. The pelletized powder was conventionally sintered for 10 h at a temperature range of 975–1025 °C, which is a lower temperature process compared to the standard solid-state reaction. X-ray diffraction analysis revealed a cubic phase for the current LCTO ceramics. The grain size of the sintered ceramics was found to increase from 1.5 ± 0.5 to 2.3 ± 0.5 μm with an increase in sintering temperature from 975 to 1025 °C. The impedance results show that the grain conductivity is more than three orders of magnitude larger than the grain boundary conductivity for LCTO ceramics. All the samples showed a giant dielectric constant (1.7 × 103–3.4 × 103) and dielectric loss (0.09–0.17) at 300 K and 10 kHz. The giant dielectric constant of the current samples was attributed to the effect of internal barrier layer capacitances due to their electrically inhomogeneous structure.

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