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Abstract: The XChem facility at Diamond Light Source offers fragment screening by X-ray crystallography as a general access user program. The main advantage of X-ray crystallography as a primary fragment screen is that it yields directly the location and pose of the fragment hits, whether within pockets of interest or merely on surface sites: this is the key information for structure-based design and for enabling synthesis of follow-up molecules. Extensive streamlining of the screening experiment at XChem has engendered a very active user program that is generating large amounts of data: in 2017, 36 academic and industry groups generated 35,000 datasets of uniquely soaked crystals. It has also generated a large number of learnings concerning the main remaining bottleneck, namely, obtaining a suitable crystal system that will support a successful fragment screen. Here we discuss the practicalities of generating screen-ready crystals that have useful electron density maps, and how to ensure they will be successfully reproduced and usable at a facility outside the home lab.

Open Access

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Abstract: XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein–ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallo­graphic software packages such as CCP4 [Winn et al. (2011[Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.]), Acta Cryst. D67, 235–242] or PHENIX [Adams et al. (2010[Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.]), Acta Cryst. D66, 213–221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

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Abstract: Diamond Light Source (DLS) provides a suite of world-leading beamlines for macromolecular crystallography (MX) experiments which are used by scientists from all over the world. Key to their success is an integrated approach to automating the hardware and software environments such that it is only necessary to enter the beamline hutch to change large batches of samples for the robotic sample changers. Alongside investing in automation, all beamlines are also equipped with Pilatus 6M-F detectors (25 – 100 Hz) resulting in fast data collections and high turnover of samples. Rapid downstream processing of the resulting data has been developed since this is essential to drive experimental decisions. The feedback from these pipelines needs to be made readily available to users in a timely manner and a number of tools are available for both local and remote visualization of results. Remote access to these facilities was a design requirement from the outset. Several tools have been integrated and developed to streamline the process of remote access yet give the same software environment remotely as would be experienced if the experimenter was present at the beamline. The advent of remote access for cryogenically frozen samples has led to the implementation of new shift patterns for the user programme, enabling frequent short shifts for the many groups who use DLS. Remote access to MX beamlines is also a prerequisite of many industrial clients of DLS. For the future we are moving forward with the development of remote access for insitu data collection from crystallization plates following on from the success of this method for screening and collecting data by users at the beamlines. The implementation and impact of remote access at DLS will be presented here.

Open Access

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Abstract: Crystal dehydration is a post-crystallization technique that can potentially improve the diffraction of macromolecular crystals. There are currently several ways of undertaking this process; however, dehydration experiments are often limited in their throughput and require prior manipulation of the samples. In the present study, a novel method is proposed that uses in situ plate screening to assess the effect of dehydration by combining the throughput of 96-well crystallization plates with direct X-ray feedback on crystal diffraction quality

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Abstract: Diamond Light Source [1] is the UK third generation synchrotron facility located south of Oxford. In the first Phase the structural biology community was served by the macromolecular crystallography (MX) beamlines I02, I03 and I04 starting with the user programme in early 2007. These widely tuneable (5-25 keV) SAD/MAD beamlines were complemented in Phase 2 with a MAD capable microfocus beamline I24 (7-25 keV) and a fixed-wavelength high-throughput station I04-1 (13.53 keV). In Phase 3 the long wavelength beamline I23 (3-12 keV), which is in the planning and construction stage, will complement the MX beamline portfolio [2]. In order to adapt to the future scientific requirements of the structural biology community and to increase efficiency, various areas of the beamlines are being improved and new techniques explored. The automation system is constantly being improved, including a quicker sample exchange with the sample transfer robot and automatic loop finding and centering procedures. All beamlines can now also be fully operated remotely. Three beamlines (I03, I04-1, I24) are now equipped with fast Pilatus detectors and it is planned to provide the other beamlines with fast detector systems as well. This leads to an increase in efficiency and throughput and allows for new methods like faster grid scans for locating hardly visible samples or to find the best area of a larger sample. Data collection strategies and crystal and diffraction image characterization are provided automatically. Very shortly after the data collection has finished the results from our automatic data processing pipeline are available and this extends now to the generation of difference electron density maps if a suitable PDB file is provided. More recently, an upgrade programme for the experimental end-stations of the Phase 1 MX beamlines (I02, I03, I04) has been initiated and is nearing completion. The completely new design allows for an easier change between experiments at cryo or room temperature or a humidity controlled setup. In-situ screening of crystallization plates is also actively being developed on all beamlines. Beam delivery to the Phase 1 beamlines will be with a refurbished bimorph KB mirror system providing typical beam sizes of 80 μm x 20 μm over the complete energy range. Furthermore, the new end-station is also equipped with two sets of compound refractive lenses (CRL) providing a beam size of 8 x 2 microns, thus enabling microfocus and standard beam size work easily on the same beamline. The implementation of a mini kappa goniometer head is being developed which will allow for more sophisticated data collection strategies. Some new developments and preliminary results will be discussed. Use of the Diamond MX beamlines has resulted in the deposition of 731 structures to the PDB so far and productivity has increased since the start of operation.