Scattering/Diffraction

Methods based on scattering and diffraction utilize the radiation that changes direction when interacting with the object. This typically provides information on length scales smaller than what can be directly imaged. In small angle X-ray scattering, samples are analyzed to obtain information about sizes, shapes and orientations of internal structures. The analyzed features are mostly in the size range 1-200 nm. For structures down to the atomic scale, X-ray diffraction is a very powerful technique to analyze crystalline samples. For example, the atomic structures of entire proteins can be resolved.

Features and Benefits

The MetalJet D2+ is the latest generation of Excillum’s patented, high-brilliance micro-focus X-ray source.  The MetalJet uses a fast-flowing liquid jet of metal instead of a solid anode metal target, thereby allowing a greater power loading to be placed on the metal target. The high-speed jet efficiently transports heat away from the interaction point and quickly regenerates the alloy. In this way, the MetalJet can generate a much higher-brilliance than conventional solid anode X-ray tubes.

You can read more about the MetalJet Technology here and find our entire MetalJet product range here!

  • Extreme microfocus source power, with ~10x higher brilliance than conventional microfocus X-ray tubes
  • Small, adjustable and well-defined X-ray spot
  • Stable X-ray emission and spot position, which is essential for long-time measurements
  • User-friendly Graphical User Interface with remote control through TCP/IP protocol for full control of source settings
  • User selectable e-beam size and position on the metal-jet enables variable take-off angle, to adjust X-ray spot size, flux and spectrum hardness
  • Advanced e-beam technology and algorithm for internal absolute spot size calibration in micrometers
  • Unique target material enables the use of characteristic lines
  • Optional dual-port mode, enables two setups from the same source
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Small Angle X-ray Scattering (SAXS)

Small Angle X-ray Scattering (SAXS)

Small Angle X-ray Scattering is used to study the structure of materials in the 1 nm to ~200 nm range. The materials typically studied include polymers, metals, colloids, liquid crystals and biological samples e.g. proteins. The information determined relates to the particle size, shape, distribution and orientation, porosity, surface features and internal structure.

A SAXS sample requires very little preparation and results are representative of the bulk material. The scattered signal is typically recorded at diffraction angles of <6° and the sample is positioned at a long distance from the detector. The measured scattered signals are accordingly extremely weak. For this reason, SAXS measurements benefit from the use of a high brilliance X-ray source such as the MetalJet, which makes weak scattering effects, stronger, more visible and more readily studied.

Examples

In-Lab SEC-SAXS for Structual Investigation of Protein Samples

  • SAXS can be used to investigate biological macromolecules especially in monodisperse solutions.

    Xenocs BioXolver equipped with MetalJet

  • However liquid bio-solutions involve structurally different molecules and complexes in dynamic equilibria.
  • SEC – Size Exclusion Chromatography has evolved as a technique to mitigate this by separating the molecules in time.
  • However this limits the measurements time window which put huge
    requirements on the X-ray source.
  • With MetalJet source in the Xenocs BioXolver system it is possible to
    perform protein in-lab SEC-SAXS even for very diluted solutions containing
    less than 1 mg of sample.

   

Application note kindly provided by Application Scientist at Xenocs SAS using a BioXolver equipped with Metaljet X-ray source.
You find the Appl. note in full here.
Bucciarelli, S. et al. Size-exclusion chromatography small-angle X-ray scattering (SEC-SAXS) of water soluble proteins on a laboratory instrument, J. Appl. Crystallogr. 2018

Fibres

Application scientists at Bruker AXS have used a NANOSTAR instrument equipped with a MetalJet (200W at 70kV) to record a series of SAXS scattering plots of a very thin fibre from a rat tail tendon. Providing intensity gains of more than 50x compared to state-of-the-art sealed microfocus tubes.

 

 

Biological (BioSAXS)

Researchers at Nanyang Technical University, A*STAR, University of Louisville, Rosalind Franklin University of Medicine and Science and Kyung Hee University have used a MetalJet equipped SAXS instrument to study the BclxL protein, a key regulator in mitochondrial calcium ion transport. The protein was treated with a mild detergent and studied during the formation of a dimer resulting from three-dimensional domain swapping (3DDS) of helices α6-α8 between two monomers.

Sci. Rep. 5, 10609 (2015), S. Rajan, M. Choi, Q. T. Nguyen, H. Ye, W. Liu, H. T. Toh, C. B. Kang, N. Kamariah, C. Li, H. Huang, C. White, K. Baek, G. Grüber, H. S. Yoon.

 

Metals and colloids

Researchers at the Slovak Academy of Science and STU Centre for Nano-diagnostics performed in-situ tests on a strain gauge, based on a monolayer of colloidal gold nanoparticles deposited on a flexible Mylar foil. The tests were monitored by SAXS where the high brightness of the MetalJet allowed a very fast data collection, with 10 seconds temporal resolution.

Sensors and Actuators A: Physical, 2016, 247, 87-95, K. Vegso, M. Jergel, P. Siffalovic, M. Kotlar, Y. Halahovetsa, M. Hodasa, M. Pellettaa, E. Majkovaa

 

Polymers

The investigation of polymers is one of the main areas of focus of the Soft Matter Analytical Laboratory (SMALL) at the University of Sheffield. Following a £2 million infrastructure investment in 2016 and the purchase of a new SAXS system with a gallium MetalJet X-ray source, their first new resulting publication was a co-polymerisation study of Styrene with N-Phenylmaleimide.

Macromolecules, 2016, 49 (18), 6731–6742, P. Yang, O. O. Mykhaylyk, E. R. Jones, S. P. Armes.

Small Molecule Crystallography

Small Molecule Crystallography

Small molecule crystallography uses X-ray diffraction in the determination and study of the three dimensional structure of a material at the atomic and molecular scale. A single crystal of the sample is required and the resulting X-ray structures provide a to scale 3D visual map of the atom types, their relative arrangement and how they are connected in space. The crystal samples studied are typically, inorganic, organic or organo-metallic compounds, primarily from research in the disciplines of Chemistry, Geology and Physics.

As small molecule X-ray crystallography becomes more automated and routine, there is increasing interest in the study of more difficult and specialist materials where a high brilliance MetalJet X-ray source is desirable. Use of the MetalJet typically means shorter experiment times, faster structures and higher throughput of samples. Small and weakly diffracting crystals, diffract more strongly providing higher quality data, whilst sensitive crystals can be measured faster with the MetalJet and suffer less degradation accordingly. Twinned crystal data can be more strongly defined using a MetalJet, making it more easily identified and potentially handled. Very weak diffraction effects, inherent to incommensurates, diffuse scattering samples, quasi-crystals and high pressure samples become stronger and may be more readily measured and investigated using the high brilliance X-rays of a MetalJet.

“The size of crystal no longer matters, no crystal is too small any longer. The MetalJet has changed the way I, as a synthetic chemist, think about crystallography”.
Professor Frank Schaper, University of Montreal

Examples

Small crystals

Tin (IV) compounds are interesting as potential catalysts and pharmaceuticals due to their biological activity. As part of a drive to understand these compounds, researchers at the Universities of Montreal, Cheikh Anta Diop and Bourgogne determined the crystal structure of a 50 μm crystal of [Sn(C2O4)Cl3(H2O)].(C4H7N2) using a MetalJet X-ray source.
• Crystal size: 0.05 x 0.04 x 0.04 mm3
• R1 = 6.2%

Acta Cryst. 2015. E71, 520–522, M. B. Diop, L. Diop, L. Plasseraud, T. Maris

 

 

Researchers at the University of Hong Kong determined the crystal structure of a tiny crystal of C23H14F3N3ORh·CF3O3S using a Bruker Diffractometer with MetalJet mounted, using Ga Kα, radiation (λ = 1.34138Å).

Crystal size: 0.04 × 0.01 × 0.01 mm3
Data collection time: 2 hours
R1 = 4.9 %
Completeness: 98.3%

J. Am. Chem. Soc. 140, 26, 8321-8329

 

Absolute structures

Application scientists at Bruker AXS used a MetalJet integrated into a Bruker D8 VENTURE diffractometer to successfully determine the absolute configuration of (2S)-(−)-2,2’-Oxybis(octahydro-7,8,8-trimethyl-4,7-methanobenzofuran), a light atom structure, where the heaviest atoms are three oxygen atoms.

• Flack x = 0.024(39) (Parsons‘)                          • Completeness: 96%
• Crystal size: 0.15 x 0.05 x 0.04 mm3              • Redundancy: 4
• Experiment time: 4 hours                                • R1 = 3.18%
• Resolution: 0.75 Å

 

Heavy absorbers

A group of researchers from the University of Montreal recently determined the crystal structure of the heavily absorbing compound [Au(PPh3) (S2CNMe2)] using a MetalJet source integrated into a Bruker D8 VENTURE. The compound was part of a study of materials based on d10 configured gold (I) compounds which have potential application in the area of luminescent sensors.
• Crystal size: 0.08 x 0.04 x 0.04 mm3
• R1 = 3.94
• Absorption coefficient μ (Ga Kα ) = 10.57 mm-1

MolBank 2017, 2017(2), M937, N. Bélanger-Desmarais, C. Reber

 

Extended metal network structures

Researchers at the University of Basel have used a MetalJet mounted on a STOE diffractometer to study the crystal structures of a series of extended three dimensional metal network structures including [Zn2Br4(L)]n. This structure exhibited long unit cell edges and a large unit cell volume of 28133.2(9) Å3.
• a = 35.9593(6) Å     • c = 25.1227(3) Å
• b = 35.9593(6) Å     • R1= 8.98%

CrystEngComm, 2017, 19, 2894-2902, Y. M. Klein, A. Prescimone, M. Neuburger, E. C. Constable, C. E. Housecroft

Protein Crystallography

Protein Crystallography

Protein crystals are extremely sensitive and poorly defined, due to the extremely large proportion of water within their structures. As a result, protein structures are ‘floppy’ and the X-ray diffraction data is typically of a much lower resolution quality compared to a small molecule structure. At the same time, the number of atoms present in a protein structure is extremely large and the data (Bragg reflections) to be collected is very closely packed together.

Protein crystallographers rely on the strongest X-ray sources to combat the issues of air sensitivity, small crystals, low diffraction and densely packed reflections. Traditionally, a high brilliance synchrotron has been used to measure full protein data leading to protein structure determination, whilst home laboratory instruments have been used for protein screening to identify the preferred crystals for measurement at the synchrotron.

High brilliance X-ray sources, such as the MetalJet have made a greater number of protein structures and experiments possible in the home laboratory, thereby accelerating research with ease of access and convenience. Using the high brilliance MetalJet X-ray source makes weak diffraction data stronger, reducing experiment times and potentially reducing sample degradation. The narrow, focused X-ray beam is ideally suited to measuring even the smallest protein crystals, providing compact and well-defined reflections. The higher intensity MetalJet X-rays typically extend the angular resolution limit of the visible protein data collected and provide more precise reflection positions and intensities, leading to higher resolution protein structures.

“The X-ray source helps a lot, in some cases its use replaces the need for synchrotron. Our main goal with purchasing and using the MetalJet is focused on studying smaller crystals. Working with 30 micron crystals is no longer an obstacle”.Dr. Jan Dohn alek, Institute of Biotechnology, Czech Academy of Sciences, BIOCEV

 

Examples

Fast data collection for high throughput screening

As an example of a fast data collection, applications scientists at Bruker AXS recorded data on a crystal of a cyclin-dependent kinase (CDK) using a MetalJet X-ray source mounted on a Bruker D8 VENTURE system.
The complete experiment lasted 200 seconds and consisted of 100° of data with the resulting 1.95 Å data allowing for a structure solution by molecular replacement.

• Exposure: 1 second                                 • Multiplicity: 3.68
• Crystal size: 0.1 x 0.08 x 0.05 mm3       • Rmerge : 6.58%
• Completeness: 97.5%                              • Rpim : 3.58%

 

 

 

Membrane proteins in-house

The successful data collection and structure solution of membrane proteins is notoriously difficult and is rarely achieved. Even rarer is the successful determination of a membrane protein structure using an in-house X-ray diffractometer system, rather than a high brilliance synchrotron radiation source.
A small crystal of GPCR (Human Orexin receptor Ox1R-StaR®) has been successfully measured at Bruker AXS using an in-house MetalJet X-ray source mounted on a D8 VENTURE diffractometer.
Data were collected in a total experiment time of ~2.5 hours to 2.77 Å resolution and the structure was successfully solved by molecular replacement.

• Scan width: 0.1°                                           • I/sigma: 8.0
• Exposure time: 6 seconds                          • Rpim : 7.62%
• Crystal size: 0.08 x 0.08 x 0.05 mm3         • Rwork/ RFree : 0.244 / 0.272
• Multiplicity: 3.2

 

 

 

 

Ligand-enzyme co-crystallisation studies

Researchers at the University of Wisconsin (Department of Biochemistry) and the National Research Council Canada, Human Health Therapeutics, recently solved the structure of WlaRA (TDP-fucose-3,4-ketoisomerase) from Campylobacter jejuni using data collected with a gallium MetalJet D2+ X-ray source.

• Resolution: 2.15 Å          • Rmerge : 7.1%
• Completeness: 99.3%     • Multiplicity: 7.1

Glycobiology. 2017, 27(4), 358-369, Z. Z. Li, A. S. Riegert, M. F. Goneau, A. M. Cunningham, E. Vinogradov, J. Li, I. C. Schoenhofen, J. B. Thoden, H. M. Holden, M. Gilbert

 

 

SAD phasing in-house

Application scientists at Bruker AXS have determined the crystal structure of Thaumatin obtained from Thaumatococcus danielii by sulphur-SAD phasing methods using data collected in-house on a D8 VENTURE diffraction system with a MetalJet X-ray source.
Using one 70 μm crystal, a complete data set was collected to 1.65 Å in <3 hours. The experimental phases were derived from the anomalous signal of the sulphur atoms and these allowed 95% of the protein backbone to be traced.

 

 

 

In-situ X-ray Crystallography

Images courtesy of Bruker AXS

In-situ crystallography is a technique in which protein crystals undergo X-ray diffraction screening and or data collection whilst in a multi-well crystallisation plate and their original growth media/conditions. Typically, X-rays are directed from one side of the multi-well plate, pass through the plate and crystal and out the opposite side of the plate, where the diffraction data are collected on an X-ray sensitive detector.

In-situ X-ray diffraction offers the following benefits:

  • Automated, rapid screening and identification of large numbers of potential protein crystals without risk of damage to the crystals
  • The identification of protein crystals from non-crystalline objects, salt crystals and other impurity crystals
  • The identification of the best protein crystals for further X-ray study

Multi-well crystallisation plates are typically of plastic construction and exhibit low X-ray transparency, high X-ray absorption and significant X-ray background scatter, all of which serve to reduce and/or obscure the X-ray diffraction signal to be studied.

The MetalJet is the ideal choice of X-ray source for in-situ X-ray diffraction in the home laboratory due to the following unique combination of technical features:

  • The potential to tune the X-ray beam size through the software, means the X-ray beam may be matched to the size of the crystal and precisely focused on to the crystal of interest, rather than a group of crystals. This also means that a much smaller area of plastic plate is illuminated by the X-ray beam leading to reduced background scatter.
  • The higher X-ray brilliance of the MetalJet combined with the lower X-ray absorption of gallium radiation; when compared with copper X-ray sources, means that the X-ray signal obtained from in-situ diffraction is greater for the MetalJet.
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