10,000 PILATUS structures in PDB

High-throughput ligand screening results in winning PDB entry

PDB entry 5PQ7
5PQ7 The 10,000th structure determined with PILATUS data.

Today, the 10,000th structure determined with PILATUS data was released by the PDB. It was determined with a PILATUS 2M detector at beamline I04-1 of Diamond Light Source. The winning entry belongs to a set of several hundred deposited by Frank von Delft's group following a project to establish a fully automated workflow for ligand screening. The first author of the deposition (PDB code 5PQ7) and the associated publication in Nature Communications, Nicholas Pearce, wins a trip for two to Switzerland and up Mount Pilatus (more info).

The first PILATUS 6M detector for macromolecular crystallography was commissioned at the Swiss Light Source in 2006, but the first system built by DECTRIS entered operation at Diamond Light Source in 2009. PILATUS detectors are not only renowned for the quality of data they measure but also for their reliability. All PILATUS 6M remain in use, though beamlines increasingly favor EIGER X 16M detectors, the new standard for cutting-edge MX.

At the current pace – more than 50% of crystal structures released by the PDB in 2017 so far have been determined with PILATUS or EIGER data – the next big celebration will take place in early 2019.

Win a trip up Mount Pilatus

The 10000th PDB entry solved with PILATUS data wins

Freeimages.com/Michael Faes
Mount Pilatus as seen from Lake Lucerne.

It started in 2006 when the prototype of a new kind of detector was installed at the MX beamline at the Swiss Light Source. Revolutionary technology led to extremely sharp spots on low background, which initially posed problems to data processing programs. Once the algorithms were improved, data of unprecedented quality helped the determination of increasing numbers of structures.

Last year, 30% of all structures released by the PDB, slightly more than 3000 entries, were solved with PILATUS data. As of this week, this has added up to a total of 9889 structures. At the current rate of deposition, we'll break though 10,000 next Wednesday.

The success of PILATUS is the foundation of our success. To celebrate the 10,000th PILATUS structure in the PDB, we invite the author to spend a few days with us in Switzerland. We've put up an exciting program that culminates in a ride up Mount Pilatus in the world's steepest cogwheel railway (small print).

Maximize your chances of winning by releasing your PILATUS structures now!

Process EIGER data with XDS fast

NEGGIA makes parallel reading of EIGER data possible

DECTRIS is proud to announce the release of NEGGIA, an HDF5 read plugin for XDS. NEGGIA presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion. Processing of HDF5 data is now as fast as processing of CBF files.

Martin Savko from beamline PROXIMA-2A of Synchrotron SOLEIL, one of the first testers of NEGGIA, is impressed: "Many congratulations for making XDS plugin so well! It is indeed delightful to see the performance of this essential piece of code in our pipeline increased by nearly 40% while keeping everything else constant."

Download NEGGIA now (registration required) and speed up your data processing.

Now detecting electrons too!

Sacha DeCarlo

Always passionate about electron microscopy, Sacha De Carlo started using EM more than twenty years ago at the University of Lausanne, where he majored in Biology and Physics in 1998. Intrigued by three-dimensional models of viruses obtained with cryo-electron microscopy data, processed on graphic workstations, he decided to continue exploring with EM and obtained a Ph.D. in biophysics in the lab of Prof. Jacques Dubochet, also in Lausanne. Sacha continued his academic career in France (IGBMC, Strasbourg) and the U.S., with postdocs in Berkeley (California) and Boulder (Colorado), culminating with a faculty position at CUNY in New York City.

Sacha left academia in 2011 and switched to industry, when he decided to work for one of the major electron microscope manufacturers, based in the Netherlands. There he was in charge of the life science applications team in the EMEAI Nanoport, the centre of technical excellence that serves as demo lab and training centre for customers as well as employees.

Born in Locarno (TI), Sacha returned to his home country and joined DECTRIS in June 2016 and is responsible for business development electron microscopy. He is working closely with the DECTRIS product development team and with EM manufacturers to deliver the next generation of direct electron detectors to the EM community.

RSNA2016

DECTRIS CEO Christian Brönnimann introduces spectral imaging

For the third consecutive year DECTRIS exhibited at the Annual Meeting of the Radiological Society of North America (RSNA) with great success. By now, our presence at the largest radiological conference worldwide has become a cherished tradition. Our lunchtime seminar was again well attended and stimulated vivid discussions. The audience felt that spectral photon counting will take radiology “Beyond Imaging”, the conference’s motto.

We look forward to meeting you again at RSNA 2017. Until then, visit medical.dectris.com to learn about the future of medical X-ray detector technology.

 

All I want for Christmas is PILATUS

SESAME starts detecting the future with a PILATUS3 300K

SESAME is the best-known synchrotron source that is not in operation. While the electrons start to orbit in the storage ring, a gift-wrapped detector “under the tree” waits for the light.

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SESAME, a new star in the Middle East.

“PILATUS3 is the first detector to arrive to SESAME. And DECTRIS is the first company to make a donation. This is excellent progress not only for the Material Science beamline, which is getting the detector, but also for the whole research center,” summarized Giorgio Paolucci, the scientific director of SESAME, during the 14th Users’ Meeting. Still, the story is more elaborate than that.

There are two remarkable aspects in the development of an international research center in the Middle East: science with its impact on the region, and the region itself. SESAME, the International Center for Synchrotron Light for Experimental Science and Applications in the Middle East, is the first center of that kind, and its political layout matches its technical complexity. Current members of SESAME are Bahrain, Cyprus, Egypt, Iran, Israel, Jordan, Pakistan, the Palestinian Authority and Turkey. The center is built in Jordan, under the auspices of UNESCO, and is supported by donations from several European synchrotron sources.

SESAME’s Materials Science beamline got its name and its wiggler from the Materials Science beamline at the Swiss Light Source [1]. A year ago, beamline scientist Mahmoud Abdellatief took over the project.

“It is an honor and a responsibility to have Materials Science as the first diffraction beamline at SESAME. It needs to serve as a true multi-purpose station, and satisfy as many users as possible,” Mahmoud reported at the European Powder Diffraction Conference (EPDIC) [2]. “We want to cover various experiments: single crystal, powder diffraction and scattering, non-ambient, time-resolved and high-resolution. But, the number of applications unfortunately clashes with our budget.”

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Even neighbours are excited about PILATUS 300K. Messaoud Harfouche, XAFS/XRF beamline scientist (left) and Dubravka Šišak Jung, application scientist at DECTRIS (right) at the future Materials Science beamline.

At DECTRIS, there was not much discussion about it. The obvious idea was to donate a fast, flexible 2D detector. After all, these detectors are already successfully utilized at many multi-purpose beamines, such as the PILATUS 2M at the Swiss-Norwegian Beamline BM01A [3] and, earlier, the PILATUS 100K at beamline 711 at MAX II [4, 5]. But, future users of Material Science need more. In order to support that many applications, the angular coverage, quantum efficiency and the speed of the detector need to be as high as possible. And in order not to impose restrictions on the choice of a future diffractometer, the weight of the system needs to be low. Since the EPDIC, lots of emails have been going back and forth before the optimal solution was found. The lightweight PILATUS3 300K system, with frame rates of 500 Hz is the perfect choice for the job.

“The system was delivered to SESAME a few days before the Users’ Meeting. This made it the best meeting I have ever attended. It was wonderful to see and hear the excitement about the detector and eagerness to get the first light,” comments Dubravka Šišak Jung, application scientist at DECTRIS.

SESAME is busier than ever. While Mahmoud is looking for a diffractometer for the MS beamline, his neighbor, Messaoud Harfouche at the X-ray Spectroscopy beamline is setting up the optics. The 14th Users’ Meeting is probably the last meeting before the first light shines from the source and proves that science can trump politics. The PILATUS3 300K came right on time. We are not going to try to prove existence of Santa. Deep down, we all know the truth, don’t we? [6] We will only wish SESAME and its users a bright New Year and lots of great PILATUS3 data.

References

[1] Willmott, P.R. et al. (2013) J. Synchrotron Rad. 20, 667–682.

[2] Abdellatief, M. et al. (2016) “The SESAME Material Science Beamline”, 14th European Powder Diffraction Conference.

[3] Dyadkin, V. et al. (2016) J. Synchrotron Rad., 23, 825.

[4] Martinez-Casado, F. et al. “Set-up for medium and high resolution powder diffraction (Ror rietveld refinement) and fast in situ studies” European Powder Diffraction Conference, 2016.

[5] Matěj, Z. et al. “Experimental advantages of Scanning 2D Pixel detectors for XPD ” European Powder Diffraction Conference, 2016.

[6] Oléron Evans, T., Fry, H. (2016) “The indisputable existence of Santa Claus (The mathematics of Christmas)”

Firmware 4.1 for MYTHEN2 released

FLATFIELD FILES TO FIT YOUR EXPERIMENTAL SETUP

The version 4.1 extends the flexibility of the systems by allowing users to upload their own flatfield files onto the system. Excellent data can now be obtained in various instrumental setups.

Modern diffractometers can be quickly adapted for a particular experimental setup by changing parameters such as filter, voltage or detector threshold. When aiming for the optimal data quality, these changes should be taken into account. This can be done by collecting a flatfield under the exact experimental conditions of your measurement, and using your flatfield for data correction.

Firmware 4.1 enables upload of four flatfield files, without overwriting DECTRIS original data. System check and interchange of active correction files take only several simple commands to the socket interface. Using the Web Client, perfect data is just a few clicks away.

 “X-ray powder diffraction technique is outgrowing its basic definitions and use. Thanks to the accuracy of MYTHEN laboratory data, we can already discuss difference Fourier maps and quantification limits well below 1%. Going further means achieving additional quality and flexibility - in current and future applications. Custom-made data correction is another step to help our customers stay ahead of their competition “ concludes Dubravka Šišak Jung, application scientist at DECTRIS.

For the upgrade of your MYTHEN2 firmware, please contact support@dectris.com.

DECTRIS achieves ISO 9001 Quality Management Certification

tl_files/root/news/0_News_2016/ISO9001_2015.jpgTo meet the needs of customers and to continuously improve customer satisfaction, even at the highest level, is the main goal of quality management and the essence of the ISO 9000 family of standards. A high level of quality and quality management is not only important to DECTRIS, but also to all of our customers.

DECTRIS has been using effective quality management processes for many years. Over the last year, we have further refined our processes to meet the specific requirements of ISO 9001:2015.

A successful audit in October 2016 has confirmed that DECTRIS’ processes meet the international standard. With efficient and well-integrated processes, DECTRIS will keep focusing on its primary mission - technological leadership in X-ray detectors for scientific, industrial, and medical applications - while incessantly improving the customer experience.
“In our 10-year history, we have always taken pride in the high quality of our detectors and customer service. At DECTRIS we are very pleased to achieve ISO 9001 certification. It shows that our commitment to quality meets and exceeds an internationally recognized and highly regarded standard,” comments Christian Brönnimann, CEO of DECTRIS, and adds: “Adhering to the ISO 9001 standard will also ensure the highest level of quality during the future growth of DECTRIS.”

EIGER X 500K Synchrotron Series

Fast, faster, EIGER X 500K

The EIGER X 500K Hybrid Photon Counting (HPC) detector utilizes the 4 and 8 bit readout capabilities of EIGER to provide never reached frame rates in a compact housing. “Until now, synchrotron experiments examining processes far below the millisecond range have only been possible via complicated pump and probe techniques. At DECTRIS we are pleased we can now empower scientists to investigate this time scale with continuous exposures and a temporal resolution of 112 microseconds”, comments Stefan Brandstetter, Product Manager Synchrotron at DECTRIS and adds: “XPCS measurements crucially depend on high temporal and spatial resolution. With small pixels and a frame rate of up to 9000 Hz with a dead time of only 3 µs, EIGER X 500K is the perfect detector for XPCS measurements.”

The system offers noise-free single-photon counting with a sensitive area of 37 mm x 77 mm and a pixel size of 75 µm. The well established control interface remains unchanged and allows for an easy and fast integration with beamline software. Complementing the ultra-fast EIGER X 500K, an economic basic model will be released that can be upgraded at any time. Both systems are available with optional vacuum compatibility.

DECTRIS AppLab opens

First light at the DECTRIS application and training laboratory

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Our diffractometer. Data collection with an EIGER R 1M in the DECTRIS application laboratory.

The DECTRIS application and training laboratory officially opened today after commissioning of the first instrument. This is a milestone in DECTRIS history and manifests our commitment towards delivering the best performing detectors for our customers, especially the growing number of laboratory users. If you are interested in testing our detectors with your crystals, please contact us to schedule a visit.

DECTRIS operates a Rigaku Oxford Diffraction XtalLAB MicroMax-003 single-crystal X-ray diffractometer with a microfocus sealed tube for standard macromolecular crystallography and small-molecule crystallography. Thanks to a partial-chi goniometer, we can collect high-multiplicity data for experimental phasing based on the anomalous signal of sulfur inherent in most proteins. The two-theta angle of up to 90° will allow us to collect small-molecule data at IUCr resolution.

We have demonstrated the performance of the instrument by quickly solving the structure of lysozyme, a common test protein, by single-wavelength anomalous dispersion. One hour of data acquisition was sufficient to obtain enough anomalous data to determine phases and autotrace the Cα backbone.

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Experimental map. Strong difference density for disulfides and clear maps obtained from S-SAD phasing of lysozyme with one hour of diffraction data.

In our application laboratory we will characterize our detectors in low-flux conditions and review data collection methods. We will strive to optimize data quality and provide the basis for the faster determination of higher-quality structures. The data acquisition software supports data collection with PILATUS3 R 100K, 200K and 300K and EIGER R 1M and 4M detectors.