ALBA Synchrotron
In the last two months, XAIRA beamline has entered in a new phase, leading to the collection of the first data sets from user samples. A great step forward in the advance of the beamline, which is getting close to its start of operation.
With the installation of the Helium chamber that encases the sample environment and the detector, last June 2024, the placement of all the beamline hardware was finally accomplished. Then, efforts moved to the commissioning of the beamline control system, the integration of the processing pipelines and the definition of the data collection procedures.
General view of the XAIRA beamline Experimental Station, upon finalisation of the hardware. Left: the Helium chamber (enclosing the detector, diffractometer and the sample environment elements) and the automated sample exchange system (including a robotic arm and the sample dewar). Right: Close up view of the robot dewar, with capacity for 29 pucks (464 pin-based samples).
As these works advanced, the beamline was able to host the first data collection experiments on real user samples. These experiments were performed using a beam approximately 10 × 10 µm2 in size; still not the expected beamsize for this beamline, but already considered to be in the microfocus range. In addition, thanks to the use of XAIRA’s Helium (He) chamber, data was collected with the sample contained in a He environment, something that will be one of the beamline’s hallmarks. Such low-density environment limits the scattering of the direct X-ray beam, which reduces the background noise that is recorded by the detector while maintaining the sample diffraction signal, ultimately leading to higher quality data.
Samples enter the Helium chamber through the robot entry valve, at the chamber ceiling. This valve is a key feature of the chamber, as it allows to maintain the Helium atmosphere while ensuring compatibility with the standard sample mounts used by cryocrystallography MX beamlines around the world. In addition, sample loading with the robotic arm takes only less than 15 seconds, enabling the high throughput that is expected at modern MX beamlines.
Once mounted on the diffractometer, the user can visualise the sample via MXCuBE-Web, a simple-to-use web app that is also employed to easily align the crystal to the beam path, as well as to configure and trigger the data collection.
MXCuBE-Web application. Sample centring screen is shown, with a ~80 µm lysozyme crystal being aligned to the beam path (indicated by a blue circle in a white circle) with the “3-click centring” procedure.
Upon completion of the data collection, MXCuBE will also automatically trigger the processing of the collected data. For rotation experiments, two types of automatic data processing pipelines are applied: a first ultrafast (below 1 minute), partial processing, for rapid feedback on the collection results, and a second complete processing, yielding full data processing up to integration of the observed intensities and refinement of all geometrical parameters. The first pipeline runs fast_dp (developed at Diamond Light Source), while the second one analyses the data with both autoproc and xia2, using a XAIRA-dedicated HPC cluster of 10 nodes (each with 24 cores running at 2,8 GHz). As these processing jobs finish, results for each collected data set are uploaded to the Data Portal, an intuitive web application (developed at ESRF) in which users can access and easily download their data and processing results. To comply with the FAIR data principles and make data easily identifiable, a unique Digital Object Identifier (DOI) is assigned to each data set. In the future, this same web will also allow users to reprocess data on the ALBA cluster.
Data Portal front-end webpage. The main page is showed, together with some of the panels that can be called for each processed data set, displaying different kind of useful information in a highly accessible way.
Using all these capabilities, several data sets have been collected at XAIRA from crystals of a viral polymerase (courtesy of Dr Ferrer-Orta, from IBMB-CSIC), resulting in high quality data, that could be processed to 2.1 – 2.2 Å.
Commissioning works continued with the collection of data from other crystal structures sent by academic research community, such those of a human RNAse (courtesy from Dr Prats, from UAB). These tests are required to identify bugs and errors in the beamline control system, which are then addressed to improve it and make it more robust. Such works with user data will continue in the following months, in preparation for the start of user operation in 2025, for which a total of 98 shifts have been allocated at XAIRA, to users from 18 different BAG proposals.