Diamond Light Source - Annual Review 2022/23

11 10 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 2 / 2 3 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 2 / 2 3 Macromolecular Crystallography Group Dave Hall, Science Group Leader K nowledge of the three-dimensional structure of biological macromolecules in concert with interacting partners, is essential to a deep understandingof their action. Theusers of themacromolecular crystallography (MX) facilities atDiamond (www.diamond.ac.uk/Instruments/ Mx.html) wish to understand biological nature and function and the many and varied tools available to them through Diamond’s MX group add significant value to their investigations. Scientists can obtain high resolution structures rapidly, and automatically, across multiple X-ray beamlines. The widest range of biologically relevant metals in proteins and nucleotides can be identified and located and additionally these can be used to solve their structures where needed. Drug discovery programmes can take advantage of the fragment based screening platform provided by the XChem facility. For users with an interest in membrane protein biology a research and training facility is available through the Wellcome funded Membrane Protein Laboratory. Room temperature studies of samples in situ from crystallisation plates or via serial synchrotron crystallography (SSX) including time resolved studies are well supported and UK SSX users of international XFEL facilities can gain further assistance with their experiments and travel assistance via the XFEL-Hub team. For the most challenging of micro-crystals the group has several facilities available and is pushing the extremes of what is feasible with X-rays and electrons with the latest instruments in development. For example, for micro-crystals excellent progress continues to be made on the electron diffraction HeXI project with successful external scientific reviews completed and a full beamline-grade Technical Design Review for phase 1 recently finalised. The instrument construction will begin imminently, and results will be used to inform the conceptual design review of the high-energy phase 2 instrument, which is scheduled to be completed by the summer. The commissioning of the newly installed hybrid pixel Quantum Detectors Merlin Quad EM 4S on the offline TF30 electron microscopes continues and recently acquired datasets are currently undergoing analysis. The HeXI project is closely linked to the sub-micron focus beamline VMXm which this year has been building its user programme via a commissioning call. Here, both academic and industrial users have been exploringwhat this unique beamline can achieve with the smallest of samples, including this year the first structures to have been experimentally phased at the beamline. Studies have included both biological macromolecules and small molecules which present different challenges to the experimental set-up. Interacting with scientists from a broad range of disciplines and varied samples is a rewarding and fruitful exercise for the beamline team through this commissioning phase to bring the beamline to a wider audience. I24 provides a dual offering of ‘standard’ MX and serial synchrotron crystallography (SSX) using a microbeam. A fully flexible beam – in both size and energy – is available with efficient data collection at high energies (> 20 keV) possible with the CdTe Eiger detector. New endstation hardware has been developed to ease switching between experimental modes. For dynamic experiments, a range of approaches are available using either LEDs, the PORTO laser system, or in situ picodroplet ejection. Complementary spectroscopic approaches have been used by several groups and new improved hardware for in situ validation of dynamic experiments is under development. Real-time assessment of serial data for users has become simpler with data collections recorded in ISPyB and automated pipelines in place providing indexing and integration of data in addition to live hit-rates. VMXi is now available to users through MX BAG and rapid access proposals. The beamline offers highly automated and remote data collection from crystals as small as 10 µm in situ within crystallisation plates. Identification and selection of crystals from optical images has recently been automated using a machine learning tool and merged multi-crystal datasets (via Dials Multiplex) are automatically available to users within ISPyB without manual intervention. Typical room temperature datasets use 3-20 crystals with structures determined to as high as 1.5 Å resolution. Grid scans to identify crystalline material within drops are available and a serial crystallography capability using a tape drive coupled with X-ray emission spectroscopy is under development in partnership with the UK XFEL Hub. A variety of studies have been published exploiting the unique wavelength range offered by the long-wavelength MX beamline I23. Significant effort has been dedicated to streamline the sample loading into vacuum and automate the sample changes inside the large vacuum end station. Experiments to wavelengths as low as 5 Å can now be routinely performed. Protocols to deal with the increased absorption at these very long wavelengths are being actively pursued. New software for analytical absorption corrections based on 3D models of the samples obtained from X-ray tomography are under development. An alternative approach is to use a high-power laser to remove the non-diffracting materials around the crystals to facilitate absorption corrections. First successful tests have been performed and over the next months we anticipate commissioning a dedicated system to become part of the I23 sample workflows for very long wavelength experiments. I04 has implemented further improvements of the dose tool for data collection and the use of dialling a target dose instead of an exposure time has been taken up by more users and has been well received with very positive feedback. I04 staffactively promote this and are providing in-person trainingon the beamline on this and other aspects of data collection. The dose information is now also displayed in SynchWeb and this allows the experimenter and I04 staff to assess if a suitable dose has been used based on the scientific aim of the experiment. This also allows for a better comparison between data sets. The use of the dose-aware data collection is even more important since a new X-ray source (CPMU insertion device) was installed on I04 in the June 2022 shutdown. This resulted in 2-7 times higher flux depending on the energy and in turn results in a much more intense microfocus beam. As a result, the detector can now be used routinely at its fastest acquisition rate of 500 Hz, increasing sample throughput, which also greatly benefits Unattended Data Collection (UDC). Furthermore, this also enables tackling more challenging samples in the microfocus regime and opens up the possibility to extend the beamline energy range to higher energies. I03 has continued to develop and offer UDC as its main mode of operation working closely with beamlines I04 and I04-1 towiden the usage of automated collection via UDC at Diamond. The ability to screen crystals for diffraction resolution prior to collecting data for the user aims has broadened the appeal and uptake of UDC by users. This allows users to select for collection if a sample meets a particular resolution requirement or to screen and collect the best of a enabled Antiviral Platform (ASAP, NIH funded) which aims to discover and develop accessible and affordable oral antivirals against COVID-19 and future pandemics. In parallel the team have been working on the flagship beamline K04 as part of the Diamond-II upgrade with the conceptual design report finalised this year. This year has seen the return of users to site not only for beamtime but also for trainingwith in particular many early career scientists havingmissed out on the opportunity to visit large scale facilities during their training programmes due to COVID-19 working protocols. The beamline teams are actively encouraging users to come on-site to experience the many changes that have been made during and after the COVID-19 pandemic and we have run our first on-site BAG trainings and Diamond-CCP4 workshop for three years. These on- site visits have provided invaluable opportunities for two-way exchange that have been much missed over recent years. range of samples. The I03 team together with experts from the SSCC group are using I03 to testbed the next generation data acquisition and analysis systems with UDC. Here new features have been developed for crystal centering using “3D grid scans”which greatly speed up and improve centering accuracy as well as open up the potential to rapidly identify multiple crystals within a single sample holder amongst many other opportunities. This new software is being developed ultimately for Diamond-II beamlines however MX users will see benefits and improvements to their future experiments before the Diamond-II upgrade with I03 at the forefront of delivering these new features. UDC has also been rolled out to beamline I04-1 this year where it is now used for all of the data collections for XChem – the fragment based drug discovery laboratory. There have been increases in laboratory capabilities this year to cope with an increase in demand from both academic and industrial users coupled with requirements to deliver for multiple international grant funded collaborations including most recently the AI-driven Structure- This year has seen the return of users to site not only for beamtime but also for trainingwith in particular many early career scientists havingmissed out on the opportunity to visit large scale facilities during their training programmes due to COVID-19 working protocols. The beamline teams are actively encouraging users to come on-site to experience themany changes that have beenmade during and after the COVID-19 pandemic