Academic and industrial researchers from around the globe use Diamond’s macromolecular crystallography (MX) beamlines to reveal and explore the three dimensional shape of large biological molecules. An intimate knowledge of shape and the arrangement of chemical properties in, for example, proteins, DNA and viruses, provides functional understanding of these important biological assemblies. This leads to better interpretation of the processes of life undertaken by cellular pathways and complex assemblies enabling discoveries spanning from fundamental biology through to MX becoming an integrated part of the drug discovery pipeline
MX is a key part of the structural biologist’s toolkit and at Diamond we provide a broad range of MX beamlines for our community to exploit this method as part of an integrated approach to structural biology. Around 60% of Diamond’s users collect data at the MX village generating significant scientific output from the operational MX beamlines at Diamond with 382 peer reviewed papers and 696 protein data bank (PDB) entries to date in 2016 alone.
Access to our facilities is by open access with a commitment to publish results via competitive peer review or confidential services on a proprietary basis via the industrial liaison office. In both cases we provide convenient routes and modes of access to our facilities with flexible shift patterns, remote beamline control and rapid access for high priority projects. In excess of 50% of all visits to MX beamlines are carried out remotely from locations throughout the world. Our vision going forward is to drive many more experiments automatically without the need for a user controlling the beamline directly. This will see another step change in how operationally effective MX beamlines at Diamond can be and how they are able to adapt to the workflow our users require to drive forward and focus on their science rather than the technique.
2016 has been a transformative year for the MX group with many projects starting to bear fruit. Operational beamlines have undertaken significant upgrades and beamlines in construction have reached significant milestones. Diamond will have seven operational MX beamlines by 2018, namely I03, I04, I04-1, I24, I23, VMXi and VMXm. At the start of 2016 we had five in full user programme mode (I02, I03, I04, I04-1 and I24) but by mid-year this had reduced to four with the closure of I02 in anticipation of its transformation to the Versatile MX in situ beamline (VMXi) dedicated to in situ data collection techniques. Consequently, there are several projects underway or completed recently to enable the four operational beamlines to maximise their efficiency and effectiveness for the user community.
At the core of maintaining our competitive edge we are moving towards intelligent fully automated high speed sample analysis, data collection and data reduction. We have a highly integrated software infrastructure aligned to state-of-the-art hardware which handles the user experiment from preparing samples through to automated structure solution. During 2016 we finished the upgrade of all our automated sample changers to the fast high capacity BART robot control system with the latest installation on I24. This has enabled adjustments to our flexible remote access shift pattern to fit better to user requirements and has resulted in 40% more time being provided to users in this mode. BART has also been essential in the exploitation of the XChem facility at Diamond and is the underlying technology exploited for automated handling in VMXi.
XChem (X-ray-accelerated Chemistry) is the new programme running at Diamond since November 2016 which spawned from a collaboration started in 2014 between Diamond and the Structural Genomics Consortium (SGC) in Oxford. It leverages on SGC sample production developments and experience as a user of synchrotron facilities coupled with the optimisation of beamline I04-1 at Diamond as a high processing capacity hub. It has the capabilities to deliver up to 30 protein-complex models per hour for users. XChem demands 1.7 days per week from the I04-1 beamtime and the first call for dedicated peer reviewed proposals was made at the end of 2016, where out of a total of 40 applicantions, 14 were selected from the UK and EU for the allocation period January to June 2017. Future calls will be aligned with Diamond beamline calls and the expectation is to ramp up operations to accommodate approximately 30 users per call. Last year I04-1 deposited 143 structures into the PDB, however in the first three months of 2017 618 were entered – more than a four-fold increase. This can be attributed to the XChem facility operating in conjunction with I04-1.
For many MX experiments the researcher wishes to use a specific X-ray wavelength from the incoming beam generated by the insertion device in the storage ring. In 2016 a significant upgrade was made to the double crystal monochromators (DCMs) of the tuneable wavelength beamlines I03, I04 (Microfocus MX beamline) and VMXi which enables the user to choose this wavelength. These have brought significantly improved stability in both short and long time frames, and rapid energy changes and have been coupled with new diamond X-ray beam position monitors with which we can control beam delivery to very high positional accuracy in an automated manner. All of these together improve the experience for users and have increased the available beam time to scientific experiments.
Over the years Diamond has invested significantly in microfocus X-ray optic capabilities to enable investigations of some of the most scientifically challenging crystals users can obtain. This year the Microfocus MX beamline (I24) which is dedicated to microfocus tuneable wavelength experiments has repolished its pre-focussing mirrors and completely replaced its microfocussing optics with superpolished mirrors and new power supplies that allow rapid changes in the focusing of the X-ray beam. Already this upgrade has enabled smaller focussed beam sizes than previously possible at I24 and ongoing work will improve this further. I04 utilises compound refractive lenses to provide microfocus beam options to its user programme. Over the last year system changes have enabled faster size changes and coupled with the improved stability of its upgraded DCM smaller beam sizes are now achievable than previously possible. Further work in the coming months will speed up these beam size changes significantly.
Taking microfocus MX experiments to the extreme, the Versatile MX mirco beamline (VMXm) aims to address challenges associated with data collection from micron/sub-micron crystals of membrane proteins and biomedically important protein complexes.It plans to do so through the development and use of careful sample preparation methods and low noise data collection techniques using sub-micron beams. The incorporation of a scanning electron microscope imaging into the VMXm end station means that visualisation and alignment of even sub-micron sized crystals will be achievable. Commissioning of the beamline optics began in spring 2017 with expectations of first experiments in early 2018.
Diamond has been a leading proponent of in situ data collection techniques for MX allowing collection of experimental data from crystals undisturbed in their growth media. I24 installed a new end station in 2015 capable of switching between cryogenic and in situ media and this has been exploited through 2016 to great effect. I03 continues to use its in situ capabilities for collecting data from biological agents up to hazard group 3 – a unique facility in Europe.
Pushing the capabilities of in situ data collection to the extreme, Diamond committed to building the first facility dedicated to this technique namely beamline VMXi. The team has worked hard to continue to run I02 whilst developing this new facility. In 2016 not only was I02 closed but the team achieved first light and users in the new VMXi facility on-time. The beamline will be fully automated with users remotely examining their crystallisation experiments in our co-located plate hotels. Once examined the users can then schedule their data collection requirements via our SynchWeb interface for ‘beamline scheduled automated screening’, data collection, and follow up analysis. A rapid turnaround of results will give timely and significant feedback to experimentalists remotely without their need to take part in the actual X-ray experiment. VMXi has the capability to revolutionise the workflow for obtaining diffraction quality crystals and data which is a major bottleneck in the MX pipeline.
The long-wavelength MX beamline I23 is a unique instrument for solving the crystallographic phase problem directly from native proteins without additional labelling1. With its extended wavelength range the positions of lighter atoms of biological importance, such as calcium, potassium, chlorine, sulfur and phosphorus can be unambiguously determined. The beamline could finally overcome the challenging sample transfer of cryogenically cooled crystals into the novel in vacuum sample environment. A variety of projects from the first set of users were successfully solved in 20162. Ongoing improvements to the sample transfer mechanism are addressing throughput and reliability.
The broad range of capabilities and experience of staff and beamlines in the MX group continue to make significant contributions to the worldwide structural biology community by bringing to life novel beamlines and significant upgrades to operational beamlines. Alongside this we run regular training courses and teaching workshops for our users to enable them to get the best from the facilities we provide.
Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.
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