23. November 2016
Collecting data with passion
A feature on serviced crystallography
On the journey from an intriguing biological question to a structure, the nights at the synchrotron it takes to collect data good enough to find answers are probably the most tiresome times for most. Hours in the dark, in front of a battery of glowing screens, the worst crystals always appearing between 3 and 5 in the morning – collecting best data is thoroughly exhausting.
As a graduate student, going to the synchrotron for the first time, things were novel, exciting and fun. After a few years, the joy has worn off for most, and data collection at the synchrotron became a dreary routine, even dreaded by some. And yet, collecting data is essential, the last experimental step in crystallography. The quality of the structure and the insight into biology are decided by it.
The situation is even starker in the pharmaceutical industry. Specialization drives structural biologists into the role of focused crystallographers whose job might be to collect countless datasets from hundreds of crystals soaked with different chemicals for fragment screening. This can be tedious work, but there are people who get excitement out of this, people who approach each new crystal as if it were their new favorite project. The best of these scientists have founded or work for companies that provide data collection as a service.
Two examples of such companies are Expose GmbH and Shamrock Structures LLC. While Expose is singularly focused on collecting data for paying customers, Shamrock Structures is a broader research services company for whom data collection is just one field of operation. Both have in common that their success depends on the efficiency and reliability with which they can collect data and on the quality of the data they provide.
Expose is based in Switzerland and calls the Swiss Light Source (SLS) its home. The labs of Shamrock Structures are near the Advanced Photon Source (APS) in Illinois, US, and most of their data are collected there. Both synchrotrons are among the most productive in the world and are renowned for the quality of their beamlines.
Joachim Diez, founder and CEO of Expose and still frequently at the beamline to collect data, is enthusiastic about SLS's approach of developing their beamlines in collaboration with industrial users. He is often among the beta testers of new features before major upgrades. "All beamlines at SLS provide the best combination of high-end technology and usability for high throughput projects", he says.
All three macromolecular crystallography beamlines at SLS operate Hybrid Photon Counting detectors. Diez prefers beamlines PXIII, whose mini-hutch design makes it the easiest to work with, and PXII, which provides the best compromise of flux and usability of the data to the customers thanks to the common CBF format that PILATUS writes.
Crystallographers at work. Shamrock Structures scientists Ardian Wibowo and Joshua Carter at LS-CAT at APS. Image used by permission of Joshua Carter, Shamrock Structures LLC.
Joshua Carter, Director of Crystallographic Data Collection at Shamrock Structures, considers APS, in particular the beamlines of the Life Sciences Collaborative Access Team (LS-CAT), the best place to collect data. The ring reliably provides X-rays of high flux and brilliance, and the beamlines are equipped with the latest technology for industrial-grade data collection, like CATS sample changers and, at beamline 21-ID-D, an EIGER X 9M detector. They also run innovative software, and hardware and software come together smoothly thanks to the hard work of exceptional beamline staff. Carter and his team are so pleased with LS-CAT that Shamrock Structures signed up as an Associate Member earlier this year.
An important factor behind this decision was the detector. All Hybrid Photon Counting detectors like PILATUS and EIGER offer superb signal-to-noise ratios but, says Carter, "I see an improvement of spot-to-background intensities with the EIGER X 9M compared to the PILATUS 6M", adding that, "there is really no comparison to be made between the EIGER and other detectors on the market."
Another feature that sets EIGER apart from PILATUS is the speed of data collection. This is more useful than just for collecting 12-15 datasets per hour. Normally, datasets are collected at 40-80 Hz, but if crystals are particularly radiation-sensitive, the speed of data collection can be increased to 100 Hz or sometimes 200 Hz. "This allows us to tailor the permissible dose better than with beam attenuation", explains Carter. "We get better data quality with increasing the speed of the data collection."
For pharmaceutical companies, the advantages of outsourcing data collection are clear. Their scientists can focus on interpreting structures and advancing drug discovery projects rather burning time collecting data. Equally importantly, the administrative burden and the logistics involved with setting up synchrotron time and the traveling to and from the synchrotron can be eliminated, and employees are more productive if they don't have to recover from nights spent at a high-throughput beamline. Any of these aspects has a clear financial reward.
Fully automated or remote-controlled beamlines exist where users can mail samples and obtain data without having to be present on site. For example, the European Synchrotron Radiation Facility provides MXpress, a mail-in data collection service, while at beamline I04-1 of Diamond Light Source, up to a thousand samples per week can be screened for bound ligands – with automatic identification of hits. Both approaches are extremely valuable for routine crystallography and high-throughput ligand screening.
When samples are of variable quality and difficult decisions need to be made during data collection, service crystallography shines. Shamrock Structures' customers benefit from the expertise and experiences of the crystallographers they work with. After collecting data for five years, with two to three twelve-hour shifts a week, Carter practically lives in reciprocal space. "I have seen more crystals and more diffraction patterns and solved more structures than entire structural biology groups at some of our customers", he says.
Diez tells a similar story. "Serviced crystallography provides the best quality in combination with the best productivity without any sample limitations", he says. Remote operated beamlines come close, but they still need local support and an expert crystallographer to collect the data and, says Diez, "well-trained crystallographers doing service crystallography combine the local support and the scientist at home."
A wall of work. Dry shippers from a large number of Expose customers are awaiting beam time at SLS. Image used by permission of Joachim Diaz, Expose GmbH.
The continued enthusiasm of Carter and Diez for their work is another plus for their customers. They signed up for data collection and for nights at the synchrotron. Where others might see tedium, they get excited by spots on a screen and the chance to get better data more quickly. They care about their customers' projects and put their vast experiences into every single one of them, fighting for superior data in every case.
Pharmaceutical companies appreciate this attention to detail and the effort put into their projects. As they pay only for the time spent collecting data, they get their results at minimal cost. This is especially true when the data are collected on a fast detector like EIGER. Small companies gain twice by not only obtaining better data than they could measure themselves but also having immediate access to a synchrotron in ways otherwise only possible for the largest players who can buy into a beamline. "Customers of any size get their data collected when they want it collected", says Carter.
Crystallographic service providers like Shamrock Structures and Expose are important players in the drive towards better data. They accelerate the process of drug discovery and help reduce cost. We at DECTRIS are excited about the role we play in this ecosystem, and we are proud of the trust Carter and Diez place in our detectors.