XtaLAB SuperNova

The XtaLAB SuperNova includes a high-flux, low maintenance microfocus sealed tube with a high precision kappa goniometer with a Hybrid Photon Counting detector (HPC), the HyPix-Bantam. The XtaLAB SuperNova can be equipped with dual sources for data collection on a broad range of sample types - Cu, Mo and Ag sources are available. The XtaLAB SuperNova control software, CrysAlisPro, allows for easy software-switching between wavelengths. The XtaLAB SuperNova is a compact, mid-range yet full-featured system that requires little servicing to maximize uptime and throughput. It is the ideal diffractometer for crystallography research laboratories.

Benefits:

  • Increase in productivity - high performance sources and HPC detector give fast results of superior quality
  • Compact and self-contained design will fit into smaller laboratories
  • Easy sample mounting and easy to use software
  • Simple maintenance due to modular design of core components
  • Eco friendly
  • Minimal downtime - supported by online diagnostics and troubleshooting

Features

  • Up to 40 W Microfocus X-ray tube with multi-layer optics
  • Easy dual-source upgrade
  • High precision 4-circle kappa goniometer
  • State-of-the-art HPC technology detector built by Rigaku
  • New protection cabinet with motion enable system. Fully compliant with EU safety directives
  • Enhanced diagnostic firmware for improved service and support
  • Powerful external PC for instrument and experiment control
  • CrysAlisPro: Powerful, user-friendly software, with optional AutoChem 3.0 for fully-automated structure solution and refinement
Rigaku's HyPix Bantam is a next-generation two-dimensional semiconductor detector designed specifically to meet the needs of the home lab chemical crystallographer. One of the HyPix Bantam's unique features is its large active area of approximately 3000 mm² with a small pixel size of 100 μm², resulting in a detector with high spatial resolution. In addition, the HyPix-3000 is a single photon counting X-ray detector with a high count rate of greater than 10⁶ cps/pixel, a fast readout speed and essentially no noise.
  • Direct photon counting with no phosphor blooming
  • Single pixel point spread function
  • 100 μm x 100 μm pixel size
  • Extremely low noise
  • Electronically gateable
  • Radiation tolerant design

CrysAlisPro — User-inspired software for superior data quality

Rigaku Oxford Diffraction systems come complete with CrysAlisPro, our user-inspired data collection and data processing software for small molecule and protein crystallography. Designed around an easy-to-use graphical user interface, CrysAlisPro can be operated under fully automatic, semi-automatic or manual control.

Automatic Crystal Screening

At the heart of CrysAlisPro are the automatic crystal screening, data collection and strategy modules. For a typical crystal, a short pre-experiment lasting less than five minutes is recorded to evaluate crystal quality. From the first frame, CrysAlisPro automatically evaluates the crystal quality and provides the user with information regarding the unit cell, intensity estimation by resolution range and suggested frame exposure times for the full data collection. Additionally, CellCheckCSD (developed with the Cambridge Crystallographic Data Center) helps prevent the collection of known structures by automatically screening the CSD for unit cell matches.

Fastest Strategy Software

CrysAlisPro's sophisticated strategy software automatically calculates the optimal conditions for fast, high quality, complete data collection. All strategies are rapidly calculated based on the specific crystal orientation and unit cell. The user has complete control to optimize the strategy for a wide variety of targets including multiplicity, time and resolution. Strategy calculations are extremely fast and efficient, allowing the user to quickly adapt the data collection conditions for a variety of experiment types, with both Mo and Cu radiation.

Automatic and Concurrent Data Reduction

Data reduction and processing initialize automatically with the start of data collection and employ intelligent routines which tune the parameters to give the best data quality. Processed data are accompanied by real time on-screen feedback of data quality and completeness. CrysAlisPro is programmed for multi-core data processing, meaning rapid results even from the largest data sets.

A Full Complement of Crystallographic Tools
In addition to automatic routines, CrysAlisPro includes a very comprehensive and highly effective range of tools and functions for dealing with non-standard and problematic data. These tools are available through the GUI or from a command line interface, and include:
  • Advanced unit cell finding
  • EwaldPro — Reciprocal lattice viewer
  • Twin data processing
  • Incommensurate data processing
  • Automated high pressure data collection and reduction
  • Face-indexing — with automated shape generation
  • Multi-temperature experiments
  • Powder data collection and processing
  • Precession image generation
  • Axial photos

Software Compatibility

Use CrysAlisPro to import and process frames from synchrotrons and other detector formats. Data is automatically output in HKLF format and quick links interface directly to Olex2, CRYSTALS, WinGX and Jana (for use of SHELX, SIR, Superflip and other programs, where installed). Data files are also easily exported for use in third party data reduction packages including MOSFLM, DENZO and XDS.

How to get CrysAlisPro

The software is freely available to users of Rigaku Oxford Diffraction systems and can be downloaded from our forum. Please register at www.rigakuxrayforum.com. Any queries related to the software may be answered on the forum.

Software Updates

We welcome user feedback and CrysAlisPro is frequently updated with new features inspired by users. In this way, our software is continually improving so that your system always provides data of the highest quality. Visit our forum for more information.


AutoChem

AutoChem is the ultimate productivity tool for chemical crystallography, offering fast, fully automatic structure solution and refinement during data collection. Developed exclusively for Rigaku Oxford Diffraction by the authors of Olex2 (Durham University and OlexSys), AutoChem builds upon the success of our original AutoChem software. Seamlessly integrated as an optional plug-in for CrysAlisPro, AutoChem offers an advanced approach for automatic structure determination, with an even higher rate of success.

AutoChem can work with or without a chemical formula, intelligently using multiple solution programs and typically requiring only partial completeness to solve routine structures. In more difficult cases, AutoChem will make attempts in multiple space groups. A number of refinement options are available; atoms are modeled anisotropically where the data supports it and hydrogen atoms are included in calculated geometric positions. The structure is then re-labeled and refined to completion before a final structure report is generated.

CrysAlisPro displays the structure and key refinement parameters, and provides a link to a full Rigaku Oxford Diffraction’s edition of Olex2 — complete with AutoChem plug-in — which can be launched at any time. Here the user can review all aspects of the refinement, step back to any stage of the process and apply changes as necessary.

The 800 Series Cryostream is the most robust, efficient and user-friendly liquid nitrogen based low temperature system available today. Specific features include a superior laminar flow system, meaning virtually zero risk of icing, extremely quiet running and a fast-start system resulting in a cool-down time to 100K of just 20 minutes.
The Oxford Cobra is the non-liquid nitrogen Cryostream. Combining the efficiency of a Cryostream with the advantages of a non-liquid system, the Cobra offers the ultimate solution for both macromolecular and small molecule crystallography.
The new micro-focus silver source, Silva, allows for measurement of charge density on samples to a resolution of 0.28 Å but an additional benefit is the ability to perform a single-theta charge density experiment out to 0.41 Å with the active area of an Atlas S2 CCD detector. Having a single theta position means fewer images and fewer runs, which improves the scaling statistics and reduces overall experiment time.
 

An experiment was performed with a crystal of diaminomaleonitrile using the Silva and the Atlas S2 CCD detector. The predicted experiment time was 54 hours when using correlated 200 second exposure times. However, due to the intelligent measurement system of all S2 CCDs any frames with overloaded reflections were automatically re-measured at ¼ of the exposure time, and the binning mode was switched from 4x4 high gain mode to 1x1 standard gain mode. This method utilises the highest detectivity mode of the detector for the weakest reflections at high angle, whilst making sure no information is lost by switching to the highest dynamic range mode for the brightest reflections. This way it is possible to collect strong and weak reflections in the same image, and maintain high data quality. In this case, because the exposure time was intentionally set to be longer than necessary, 267/458 frames were automatically re-measured. This increased the experiment time by less than 10%, by only re-measuring individual images that contained overloaded reflections without adding extra runs to the experiment.

Experimental details
Experiment time (hrs)59
Correlated exposure time (s)200
Rint (∞ – 0.4 Å)0.055
Rint (∞ – 0.8 Å)0.020
I/σ (∞ – 0.4 Å)8.7
I/σ (∞ – 0.8 Å)29.6
R1(%)5.49
Table: Statistics for charge density experiment measured on diaminomaleonitrile, which was kindly provided by Prof Chris Frampton, Brunel University, UK
Figure: Crystal picture and refined structure of organic sample from charge density experiment.
Rigaku Oxford Diffraction has a range of high-flux, low maintenance microfocus sources to suit even the most challenging of samples. The new microfocus silver source, Silva, extends the potential sample range even further and is suited to highly-absorbing samples. The shorter wavelength of the silver source (0.56 Åcompared to 0.71 Åfor molybdenum) means that the absorption coefficient (µ) of most samples can be approximately halved. The table below shows the statistics for a crystal kindly provided by Wroclaw University, Poland that was run on Mo and Ag microfocus sources with an 18 hour time limit. Although the redundancy was lower for the Ag data due to the longer exposure time per image needed to achieve good statistics, the reduction in absorption actually increases overall I/s, and improves the final R₁ value.
Figure: Crystal image with wireframe model used for the numerical absorption correction, and final structure model
Mo (μ = 20 mm⁻¹) Ag (μ = 11 mm⁻¹)
Exposure Time per frame (s)2040
Redundancy170130
I/σ2534
R1(%)2.291.28
Table: Details of experiment run on inorganic Y₃Al₅O₁₂ crystal with Ia3d symmetry. Microfocus Mo and Ag sources were used for both experiments and full face-indexed absorption correction applied via CrysAlisPro.
Some geological samples are so highly-absorbing that it is very difficult to get a good refinement, even with a Mo data collection. The new micro-focus silver source, Silva, gives excellent data on these very highly-absorbing samples. The crystal in the following example has a µ of 47 mm⁻¹, even at the silver wavelength. However, when measured on a SuperNova with the new silver source, a good quality refinement was achieved with 16 hours of data collection time.

Figure: Structural model of geological sample, which contains an OPb₄ oxo-centred array with alternating Pb-Si-O and Pb-As-O bearing slabs, as well as mixed metal-O4 sites.
 
Experimental details
Exposure time (s)120 + 20
Resolution (Å)0.56
I/σ9.29
Rint 0.026
R1(%)5.5
Table: Statistics from 16 hour experiment performed on a very highly absorbing sample, chemical formula As₅Cl₁₈MoO₇₄Pb₆₄SiV. The sample was kindly provided by Dr Mark Welch, Natural History
The shorter wavelength of Ag compared to Mo and Cu allows more reflections to become accessible in the limiting window of diamond anvil cells (DACs). This is a huge advantage when it comes to solving the structure with incomplete data. A single crystal of 2,2-dimethylbutane or DMB were grown from liquid in a DAC at Warsaw University. The sample was then measured using the Silva source at 2.7 GPa having the space group Pnma. A completeness of nearly 60% was achieved out to 0.8 Å with a final R1 of 5.0%. Many thanks to Roman Gajda, Warsaw University, Poland for providing the data.
Figure: Example image of DMB crystal experiment performed with Ag radiation at 2.7 GPa, and the final refined structure.
Since the introduction of CCD based area detectors for X-ray crystallography molybdenum has often been put forward as the best choice for a general purpose diffractometer system. The ever-growing popularity of dual source systems has enabled many chemical crystallographers to gain experience with copper as well as molybdenum sources. Here we compare the Mova and Nova micro-focus sources.

Data Collection Challenge – Mo and Cu Data Sets Collected With a 1-Hour Time Limit

In order to compare the Mova (Mo) and Nova (Cu) micro-focus sources, a small organic crystal was measured on both wavelengths with a total data collection time limit of 1 hour. The challenge was to observe whether or not both wavelengths could provide data of sufficient quality for publication.

Experimental

Small sample crystal (encapsulated in glue) with approx. dimensions 0.044 x 0.059 x 0.102 mm
The crystal was mounted on a dual source SuperNova equipped with the large area Atlas CCD detector. Two data sets were then collected, one with Mo radiation and another with Cu radiation. The experiments were carried out consecutively on the same diffractometer to ensure the experimental conditions and crystal orientation did not change. Using the CrysAlisPro strategy module, which has been carefully optimized to produce efficient collection strategies quickly for either Cu or Mo radiation, a 1 hour data collection strategy was devised for both wavelengths. The goal was to first attempt to collect complete data (98.5% or better) up to a minimum resolution of 0.84 A° (2? = 50° for Mo, 133° for Cu) then to consider diffracted intensity. The frame exposure times were tuned to achieve this, meaning that under the time constraint applied, I/s statistics for each dataset could then be used as an indication of the relative performance of the two sources.
Data collection parameters for Mo and Cu data sets
Molybdenum Copper
Wavelength0.7107 Å1.5418 Å
Temperature296 K296 K
Min Exposure Time  (including retakes)5.5 s1 s
Max Exposure Time22 s6 s
Detector Distance53 mm53 mm
Scan Width
Total Frames77650
Total Time1 hr1 hr

Results

Using an average I/s of 2 as an indication of the diffraction limit, the copper data set diffracts beyond the intended target of 0.84 A° whilst the molybdenum dataset only reaches approximately 1.06 A°. The effect of this carried across to other data quality indicators such as Rint and the conventional R-factor (R1).
  Structure of N-hexyl-1,8-naphthalimide
Data quality indicators from 1 hour data sets
Molybdenum Copper
Diffraction Limit [I>2σ(I)]1.06 Å0.84 Å
<I>880.6119499
<I/σ>4.516.12
Rint [all data]8.60%5.20%
R1 [all data]7.45%5.85%
Conclusion
In this case the structure solves and refines easily for either data set. However, the poor effective resolution limit of the molybdenum data set (1.06 A°) would require justification in order to publish the data. The copper data is much stronger and therefore has no such problems. This fits the general trend that whilst copper data sets require significantly more frames to achieve the same level of completeness, exposure times are shorter and the data obtained in the same overall time is typically better than corresponding molybdenum data. It is therefore no surprise that high intensity copper sources are increasingly being used in routine chemical crystallography as well as in more traditional applications such as absolute configuration studies and protein crystallography.
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