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 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 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.

Masquerade: removing non-sample scattering from integrated reflection intensities

2012 ◽  
Vol 45 (2) ◽  
pp. 292-298 ◽  
Author(s):  
J. A. Coome ◽  
A. E. Goeta ◽  
J. A. K. Howard ◽  
M. R. Probert
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Low Temperatures ◽  
Test Case ◽  
X Rays ◽  
Atmospheric Conditions ◽  
X Ray Diffraction ◽  
New Approach ◽  
X Ray ◽  
Internal Agreement

X-ray diffraction experiments at very low temperatures require samples to be isolated from atmospheric conditions and held under vacuum. These conditions are usually maintainedviathe use of beryllium chambers, which also scatter X-rays, causing unwanted contamination of the sample's diffraction pattern. The removal of this contamination requires novel data-collection and processing procedures to be employed. Herein a new approach is described, which utilizes the differences in origin of scattering vectors from the sample and the beryllium to eliminate non-sample scattering. The programMasqueradehas been written to remove contaminated regions of the diffraction data from the processing programs. Coupled with experiments at different detector distances, it allows for the acquisition of decontaminated data. Studies of several single crystals have shown that this approach increases data quality, highlighted by the improvement in internal agreement factor with the test case of cytidine presented herein.

scholarly journals XAS at the Canadian Macromolecular Crystallography Facility

2014 ◽  
Vol 70 (a1) ◽  
pp. C1525-C1525
Author(s):  
Julien Cotelesage ◽  
Pawel Grochulski ◽  
Michel Fodje ◽  
James Gorin ◽  
Kathryn Janzen ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Minimal Risk ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Biologically Relevant ◽  
Wide Range ◽  
X Ray Absorption ◽  
Do So

Recent additions to the Canadian Macromolecular Crystallography Facility have expanded the capabilities of its bending magnet beamline. It is now possible to perform x-ray absorption spectroscopy (XAS) on crystals. A wide range of biologically relevant metals can be further studied, supplementing diffraction data. XAS can be used to determine if metalloproteins are photoreducing during diffraction data collection. The geometries of metal complexes can also be inferred with near-edge and EXAFS data, often more accurately than crystallography. CMCF-BM can be employed to do the abovementioned techniques on powder and solution samples that contain a metal of interest. One XAS-based technique that shows promise is single crystal plane polarized EXAFS. This technique combines crystallographic data with the findings from XAS to yield a high resolution three dimensional atomic model. More recently a number of the procedural steps required for the acquisition of XAS-based data have been automated in the MxDC software suite. These changes to data collection make it easier for users new to these disciplines to run the XAS-based experiments. By having the necessary equipment to do XAS at a protein crystallography facility, researchers who may not have had the opportunity delve into the field of XAS now can do so with minimal risk in terms of materials, funds and time.

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.

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