Skip to main content

MD3-UP X-Ray Diffractometer – MX crystallography

This video presents the MD3-UP X-Ray diffractometer installed on the MX beamline ID 23-2 (MX crystallography beamline, ESRF synchrotron)
The MD3-UP is a co-development of the European Molecular Biology Laboratory (EMBL) and Arinax Scientific Instrumentation.

High Precision Single Crystal Diffractometer

200 nm Sphere of Confusion
With its 200 nm sphere of confusion (SOC) the MD3 sets new standards in MX crystallography at synchrotron based beamlines.
The extraordinarily small SOC at high rotational speed is not only valid for the Ω-axis as a sole mechanical set-up but for the entire pile of mechanical axes: an xyz-alignment table supporting the Ω-axis and an additional xy-sample centering stage on top of the Ω-axis.

Exceptional accuracy
The MD3 Ω-axis features a superior accuracy perfectly suitable for advanced data collection strategies like helical & grid scans. The Ω-axis combines a static precision of ±0.5 mdeg and an exceptional dynamic precision of ±0.7 mdeg (@10 deg/s rotational speed, with a mounted SmartMagnet-goniometer head).

A vertical Omega axis
Due to the vertical Ω-axis geometry gravitational effects does not affect the SOC. Even when using a kappa-goniometer head the SOC remains exceptionally small.
The MD3 diffractometer is available in two orientations, the MD3-DOWN and the MD3-UP, with an Ω-axis pointing either downward or upward. The MD3-DOWN is ideally suited for experimental configurations with 6-axes sample changer robots using vials with SPINE sample pins. The MD3-UP has the advantage of free space above the sample, giving easy access to the sample position.

On-Axis Video microscope B-ZOOM

The MD3-UP integrates the new On-Axis Video microscope (OAV B-ZOOM) for precise sample and beam spot visualization. As its predecessor, the OAV B-ZOOM allows to perfectly align the sample with respect to the center of rotation and the X-ray beam. The OAV B-ZOOM is an hybrid zooming system allowing instant zoom change and integrating a multi-camera video server.

This patented video microscope is controlled within the MD3 software and combines high image quality with parallax free imaging and advanced software functionalities like the “3 click sample centering”.

See More About The OAV B-ZOOM

Advanced technology to optimize data acquisition

X-ray beam devices
The MD3 integrates multi-adjustable tools which can be moved into or out of the beam. These tools are positioned along the beam path before and after the sample, e.g. the beamstop in the latter case. These different tools are the beam shaping apertures, a background reducing capillary, a scintillator-photodiode pin for beam characterization and a movable beamstop with variable beamstop-to-sample distance.
All these integrated tools are fully controllable within the MD3 software which assists and supports the user with features like the beam location or sample alignment & centering.

Assisted beam location, alignment & centering
The MD3 software has a “3 click sample centering” system which exploits the OAV performance. With only three clicks the user can:
– Localize the beam, thanks to a beam picture provided by the scintillator
– Align the sample to the beam position
– Center the sample within the beam

4D data collection strategies: Helical Scans, Grid Scans & Serial Crystallography

Dedicated to modern MX crystallography beamlines, the MD3 offers many advanced data collection strategies:

The Ω-axis is mounted on an alignment table with three linear and orthogonal axes, the so-called xyz-alignment table. Two linear tables, perpendicular to itself and the Ω-axis, are mounted on top of the Ω-axis. This is the so-called xy-centering stage.

Finally, the sample holder or any other goniometer head, e.g. the Mini-Kappa MK3, is mounted onto the xy-centering stage. All of these different motorized axes can be moved simultaneously and are controllable in real-time. This is exactly what is necessary for 4D data collection strategies.

Combined with high accuracy and dynamic precision for all of these motion elements the MD3 becomes the ideal high precision goniometer for modern MX-diffraction techniques like helical scans, grid scans and serial crystallography.

These advanced control features and scan-types are integrated and fully supported by the MD3 control software.

Helical scans
A helical scan consists in an oscillatory movement with the Ω-axis while scanning the sample with a series of linear movements. These combined movements result in a helical sample trajectory.

The aim is to entirely scan the crystal with a limited impact due to radiation damage. This method is especially adapted to elongated or needle like crystals, (Gabadinho, 2010), (Flot, 2010).

Grid scans
The grid scan method consists in scanning a crystal according to a virtual grid: each cell of the grid has a dimension close to the x-ray beam size. Each cell is irradiated with a sufficiently low x-ray dose and diffraction images are recorded. Then, the diffraction power is mapped for the entire grid.

The main application is to find the area of a crystal which is best suited for data collection. The diffraction power map allows selecting the best diffracting crystal area.

This method is also well-suited to locate small diffracting crystals on a sample support with many crystals. This second application is not restricted to special sample supports and can be used with standard loops or crystallization plates (in situ). (Song, 2007), (Stepanov, 2011)

Serial Synchrotron Crystallography (SSX)
Serial synchrotron crystallography is a method that combines the advantages of grid and helical scans: thousands of small sized crystals (0.2 to 5 µm) randomly distributed on a single sample support are scanned in only one operation. Then, the collected diffraction data from all of these crystals is merged in a single data set (Gati, 2014).

Serial synchrotron crystallography is a very powerful diffraction technique which overcomes the difficulties of x-ray data collection from micro-crystals.

Having specific questions about MD3 and Serial Crystallography?

Contact us!

Enhanced functionalities

Advanced Detector Trigger modes
Recent X-ray detectors integrate several trigger modes for synchronization with the MX goniometer. The MD3 is compatible with the classical single trigger mode, but it is also fully-compatible with the multi-enable mode.
The MD3 provides continuously the exact position/orientation to the detector: consequently, each diffraction image is tagged with the crystal’s position and orientation.
This functionality is available for all crystallography methods, including advanced data collection strategies.

Mini-Kappa MK3

The MiniKappa, MK3, is an easy to mount/dismount goniometer head which offers an additional kappa and phi axis. This gives numerous possibilities of crystal re-orientation in a fast and easy way.
Together with the software package STAC the MK3 allows setting up crystal alignment strategies which lead to more efficient x-ray data collection (Brockhauser, 2013).

See more about the Mini-Kappa

In situ crystallography

An optional goniometer head, the Plate Manipulator, for the reception of 96-well plates enables in situ experiments to be done with the MD3. This goniometer head is fast and easy to mount/dismount. It is equipped with an extra motorized axis. Mounted onto the MD3 Ω-axis, any crystal, even small sized, can be reached with high accuracy in any of the 96 wells, e.g. for in situ screening.

See more about the Plate Manipulator

 Arinax & Beamline Integration

For over 12 years now Arinax has developed strong competences in beamline integration. Thanks to this strong expertise, Arinax can entirely integrate the MD3 to beamline specific software like MXCube or Blu-Ice. To do so, the MD3 software is fitted for multi-device servers: TINE, TANGO and EPICS.

In addition, the MD3 is fully configurable for automated beamlines using sample changer robots, like the ones distributed by IRELEC-ALCEN.

request more information
MD3 -UP diffractometer on MX beamline ID23-2 – ESRF (2017)

Technical specifications – MD3-UP Configuration

Ω axis Vertical
Ω Scan axis
Sphere of confusion
(with SmartMagnet Nozzle)
200 nm radius, @ 100 deg/s *)
Sphere of confusion
(with MiniKappa Nozzle)
200 nm radius, @ 100 deg/s *)
Max. Rotation speed 720 deg/s
Design angular resolution 0.1 mdeg (full step)
Static accuracy Below ± 0.3 mdeg
Dynamic accuracy Below ± 0.7 mdeg @10 deg/s
Sample alignment (AY,AZ): Raster / Grid scans axes
Design resolution 5 nm
Range AY: 108 mm
AZ: 6 mm
Static accuracy (on load) Below ± 100 nm
Dynamic accuracy (on load) Below ± 1µm @ 15 mm/s on AY
Below ± 1µm @ 1 mm/s on AZ
Grid U-turn delay < 300 ms @ 15 mm/s on AY
Centering table (CX,CY): Centering, Helical Scan axes
Design resolution 5 nm
Range CX, CY: 5 mm
Static accuracy (on load) Below ± 100 nm
Dynamic accuracy (on load) Below ± 1µm @ 0.8 mm/s on CX,CY
Beam aperture
Diameter range 5 selectable diameters, Min: 5 µm
Resolution 16 nm
Repeatability Below ± 1µm
User interface JAVA Control application
Beamline software integration Customizable (e.g. MXCube, Blu-Ice)
Multi-device servers TINE, TANGO, EPICS
Sample changer robot Robot hardware & software integration
Control features

Parallax-free sample visualization

semi-automatic sample centering

4D Data collection strategies

Advanced detector synchronization modes

Selectable beam shaping tools

On Axis Video microscope (OAV B-ZOOM)
Design resolution 0.16 µm/pixel
Resolving power USAF target 1951, group 9.2 (575 lines per mm resolved)
Video Server bandwidth >= 20 FPS (depending on network)
Movable beam-stop
Distance to the sample 25 to 77 mm
5 to 57 mm
Beamstop diameter 300 – 400 – 500 µm
Power Supply
Voltage 110 VAC to 240 VAC
Frequency 50 to 60 Hz
Electric power 1000 W
Dimensions (W,H,D)
Depth x Width x Height 225 x 600 x 600 mm3
(Support Feet can be added)
Diffractometer only 80 kg

For more information about capillary, beamstop, motor reference, … See our download webpage.

Having a specific request? e-mail us!

*) with efficient vibration dumping and including measurement noise correction