A new generation of Crystallographic detector for Multi-user Barkla X-ray laboratory

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

X-ray crystallography offers the opportunity to observe highest level of details in protein and RNA/DNA molecules. It has delivered unrivalled knowledge of many biological processes including respiration, photosynthesis, cell signalling, receptor's activation and enzymatic mechanisms. The way we think of biology and biological processes has transformed due to our ability to determine high-resolution structures of even the most complex systems. It also has revolutionized modern drug discovery and structure-based drug/lead-compounds have become a commonplace.

The tremendous success of X-ray crystallography over the last 30 years has largely been due to the availability of highly intense Synchrotron Radiation (SR) facilities. During the last couple of decades, the SR sources have seen tremendous progress in the performance in terms of brightness where the brightness gain has been twice as fast as the rate of improvement in semiconductors (Moore's law), The increasing X-ray photon density delivered by the increasingly brighter sources has required rapid development in beamlines, optical elements and detectors. A major improvement in detectors from photographic plates to image plate to Charged Coupled Detectors (CCDs) emerged at the end of last century. DIAMOND Synchrotron opened its operation with MX beamlines using large CCDs but all of these have been replaced by photon counting hybrid pixel array silicon detectors (HPC) - in fact DIAMOND set the pace of change capitalizing on the development of HPC detectors that originated at the Swiss Light Source.

The laboratory sources have continued three important roles, namely (i) pre-screening of crystals, their initial characterisation and establishment of soaking conditions of ligands/compounds/inhibitors, (ii) determination of structures of well diffracting systems (in fact the number of structures determined using laboratory sources per annum currently is the same as in the 1980s/90s) and (iii) train and equip PhD students and PDRA with in-depth skills not just in the use (as a user) but acquire in-depth understanding of instrumentation as well as the subtleties of data collection. The laboratory sources (and associated optics) have also improved and detector technology is also advancing but a decade or so behind the synchrotron. Only recently the technology of photon counting hybrid pixel array silicon detectors has become available for laboratory sources at a fraction of the price compared to detectors that are being bought for synchrotrons. This reduction in price has been achieved by matching the specifications of these new generations of HPC detectors to the laboratory sources.

X-ray detectors must collect, quantize and digitize incoming X-rays while preserving highly precise location information. State-of-the-art new generation HPC X-ray detectors can collect X-rays with exceptional (>99 %) quantum efficiency. In recent years reduction of pixel size has increased the quality of the data collected; similar to increasing screen resolution in high definition televisions. Dectris have led the way in hybrid pixel array detectors and their new EIGER range combine small pixel size with high quantum efficiency and signal to noise. The EIGER R range is tailored for more intense laboratory sources and is capable of high-count rates with continuous readout and have small (75 microns) pixels, similar to our current MAR225CCD, which is now 12 years old. The provision of this latest generation of detector will not only ensure continued successful operation of the Barkla laboratory but also will enhance our capabilities for weekly diffracting systems including membrane protein crystals and multi-component complexes.

Technical Summary

The Barkla X-ray laboratory established in 2011 equipped with MAR225 CCD has provided an extremely useful capability for screening crystal and optimising conditions prior to data collection at advanced facilities of DIAMOND and SOLEIL. This has allowed us to expand the structural biology programme across the institute and beyond in a fairly short period. It has also allowed us to address some of the challenging biological problems including a number of membrane proteins. The CCD detector is now 12 years old and is suffering from reliability issues and requiring significant maintenance.

HPC detectors are photon-counting detectors and have ONLY recently become available for laboratory sources. The EIGER R series is the latest generation of HPC detectors that feature auto-summation, which extends their digital counting ability up to more than 4.2 billion counts per pixel with unrestricted dynamic range. Moreover, the EIGER R 4M delivers these high-count rates with continuous readout, achieving duty cycles greater than 99%. The EIGER R 4M detector has small (75 microns) pixels, similar to our current MAR225CCD. With its single pixel point spread function, EIGER provides superior resolving power for reflections from samples with long unit cells and as such one can reduce sample-to-detector distances by 20% than those used for CCDs or PILATUS detectors. Given the high counting efficiency and small pixel size, we plan to upgrade next year our MX optics from the current HF to RIGAKU's VHF optics that will provide a focal spot of 100microns. This staged development will ensure a highly effective in-house capability for the next 6 to 8 years.

This new generation of MX detector will maintain the Barkla lab at the cutting edge allowing the strengthening of structural biology programme and supporting the BBSRC funded projects well into the next decade. The facility will provide critical infrastructure for many research groups and generate new science programmes.

Planned Impact

The acquisition of a new generation of MX detector will allow BAKLA X-ray laboratory to remain at the cutting edge and will continue to strengthen structural biology programme in Liverpool. Availability of an up to date in-house research equipment allows University groups immediate access for regular testing of crystals, and their optimisation and exploring soaking conditions of ligands/substrate/partner proteins in an iterative manner prior to synchrotron visits. In this way precious synchrotron time can largely devoted for the well-characterised systems with positive outcomes. The availability of new generation of MX detector at the Barkla laboratory at the University will continue to contribute to the development of next generation of structural biologists (PhD students and PDRA) to acquire in-depth skills not just in the use (as a user) but acquire in-depth understanding of instrumentation as well as the subtleties of data collection. They, in turn will be able to become the next generation of card-carrying crystallographers equipped to contribute to new imaginative solutions in the future, keeping UK at the forefront of macromolecular crystallography.

The MX facility equipped with the new generation of HPC detector EIGER R 4M will have broad users base which we expect to double in numbers in the next 3 years. The proposal already represents 15 academics and their research groups so the equipment is likely to have a significant impact on the science programme and capability of some 100 researchers (half of whom are likely to be PhD students) in the next 3 years.

We are fully committed towards the RCUK's goals and objectives in maximising the use and impact of its strategic equipment. We will ensure that the equipment/facility and the scientific expertise embedded therein are made fully available to all UK/N8 academics, and that (where appropriate) training of external staff is central to the delivery plan of the BARKLA laboratory. We plan to hold a hands-on workshop for immediate users followed by an extended workshop to the wider community of N8 universities and beyond.

We will continue to work with instrument manufacturers including DECTRIS (the supplier of EIGER R 4M) who are contributing 21% of the cost of the detector, RIGAKU and MarExperts who helped us establish the Barkla laboratory. The detector will be incorporated on the MAR DTB system and may lead to long-term collaboration between DECTRIS and MarExpets. Similarly the use of this new generation detector on RIGAKU's X-ray source in Barkla may provide pilot data for RIGAKU that may catalyze further collaboration in improving the capabilities of home sources including those at BARKLA through for example a better matched optics.

We will work with academic users and instrument manufacturers through hosting of N8/UK researchers in our laboratory for frontier technologies and showcase our capabilities at regional, national and international crystallography and biophysics meetings in 2017/18. These mechanisms will facilitate new interactions with a range of stakeholders leading to new applications, scientific developments and inward investment.

Publications

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Description New detector allowed UoL structural biologists (PIs, PDRAs and PhD students to do routine and regular testing of crystals, soaking conditions of ligands/substrate/partner proteins, establish and refine cryo- conditions in an iterative manner and optimise the system prior to synchrotron visits where the team can focus in collecting highest resolution X-ray diffraction data that is possible. Thanks to use of the facility many research questions has been answered such as drug candidate molecules were visualised bound to dtrug target or ligand binding propertied of the proteins were established and novel disease related protein structures were obtained.
Due to the most up to date data collection capability the Barkla X-ray laboratory is continuing to allow the development of next generation of structural biologists (PhD students and PDRA) to acquire in-depth skills not just in the use (as a user) but acquire in-depth understanding of instrumentation as well as the subtleties of data collection. The training of new generation of structural biologists is an important contribution to society.
Exploitation Route In addition to being out standing experimental facility, the laboratory is also excellent show case for undergraduate students, and and school visitors, though tjis was not possible last year due to COVID-19.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Other

 
Description We already engage strongly with instrument manufacturers from Dectrix and MARexperts, assisting them in the authoring of specialised application notes and adapting instruments for new capabilities by hosting industrial colleagues in our groups to assist in technology development. We work with both academic and commercial users through hosting of partners in our laboratory for frontier technologies and showcased our capabilities at regional, national and international crystallography and biophysics meetings (IUCR congress Hyderabad India 2017, EBSA congress 2017 Edinburgh, UK, MND meeting 2019 and we will also show case the results at IUCR congress 2020 Praga).
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Electronics,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
 
Title mardtb at Barkla Lab upgraded with EIGER R 4M 
Description An EIGER R 4M detector has been installed in the Barkla X-ray Laboratory of Biophysics at the University of Liverpool. This is the first EIGER R 4M to be operated on a mardtb. Made by marXperts, these goniometers continue to impress with innovative features. In the past, relatively slow image plates were the detector of choice for laboratory applications. Upgrading them with a fast, noise-free Hybrid Photon Counting detector is a straightforward way of raising the performance of the diffractometer. 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact The equipment is listed on the University equipment database, which is made available to all RCUK listings and the Shared Research Equipment Inventory (www.n8equipment.org.uk). We will also register the equipment on equipment.data.ac.uk which has been set up to enable access to UK research equipment. The photon counting capability EIGER R 4M detector permits even weaker diffracting systems to be measured. 
 
Description Shrewsbury School visit and open days 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact 160 pupils from Shrewsbury School attended the research facility to facilitate the interest of school kids to biology. 100 pupils interested in biochemistry visited the lab over 3 open days in 2017-2019, some were potential students who already received an offer from Liverpool, some just interested in science. Most of them did not hear about protein crystallography before the visit.
Year(s) Of Engagement Activity 2017,2018,2019