High-throughput crystallisation and ligand screening

EMBL Grenoble’s High Throughput Crystallization and Fragment Screening Facility (HTX lab), offers access to fully automated, remote controlled crystallography pipelines based on the CrystalDirect technology and the CRIMS software.

This unique facility is one of the core technical platforms of the Partnership for Structural Biology (PSB) and is available to external users via iNEXT-Discovery project and INSTRUCT-ERIC.

EMBL Grenoble operates the High Throughput Crystallization Facility (HTX lab), a large scale user facility offering High Throughput (HT) crystallography services. Since the start of operations in 2003 the HTX lab has provided services to over 800 scientists and processes more than 1000 samples per year.

The HTX lab has a strong focus in the development of new methods in macromolecular crystallography, including methods for sample evaluation and quality control and the creation of the CrystalDirect technology, enabling fully automated crystal mounting and processing.

The HTX lab has also developed the Crystallization Information Management System (CRIMS), a web-based laboratory information system that provides automated communication between crystallization and synchrotron data collection facilities, enabling uninterrupted information flow over the whole sample cycle from pure protein to diffraction data. This software is currently in operation in multiple laboratories across Europe

Through the combination of the CrystalDirect technology and the CRIMS software, the HTX lab has developed the concept of Online Crystallography: fully automated, remote controlled crystallography pipelines integrating crystallization screening, crystal optimization, crystal mounting and cryo-cooling, and automated X-ray data collection (at ESRF, PETRA III and SLS synchrotrons) into continuous workflows controlled though dedicated web interfaces. This approach minimizes the delay between crystal growth and measurement, accelerating the progression of challenging projects. The CrystalDirect technology also enables automated crystal soaking making it possible to support highly efficient automated, large-scale small molecule and Fragment Screening by crystallography.

scientific poster
Illustration of the concept of Online crystallography.

HTX Lab

Currently The HTX Lab  offers access to the following pipelines:

X-ray diffraction data collection is typically carried out at the Macromolecular crystallography (MX) beamlines of the European Synchrotron Radiation Facility (ESRF) operated by the ESRF- EMBL Joint Structural Biology Group and at the Petra III synchrotron.

In collaboration with the Synchrotron Diffraction, Instrumentation and ESRF MX Teams, the HTX lab is working towards integrating the CrystalDirect technology into the MASSIF-1 beam line environment, which will now be operated in coordination with the HTX Lab. This will increase our throughput and capabilities to support fragment screening and online crystallography. At the same time, it will enable new experimental opportunities.

Moreover, we will continue to develop the CrystalDirect technology to support serial crystallography applications as well as new approaches for the rapid analysis of membrane proteins both at cryogenic and room temperature.

For applications please contact José Marquez, head of the Crystallisation Facility.

Description of the platform

Specific equipment

The EMBL Grenoble HTX Lab is equipped with a nanovolume crystallization robot (including an LCP module that enables crystallization of both soluble and membrane proteins), an Echo Labcyte acoustic dispensing system, for the delivery of ligand solutions, crystal farms (at 5 º and 20 º), two robotic liquid handling stations to prepare crystallization screenings, and two automated CrystalDirect crystal harvesters with capacity to produce and store up to 400 frozen crystals per operation cycle.

The facility is operated by dedicated technicians. In the last years, and in a collaboration with the Global Phasing consortium, the facility has introduced capabilities for in line crystallographic data processing. Dedicated data storage and processing servers with capacity for 150 Tb and 84 CPUs respectively have been implemented to support data analysis.

Our services include: primary crystallization screening, crystal optimisation, automated crystal harvesting and processing and data collection in collaboration with the ESRF and PETRA III synchrotrons, as well as support for data analysis. Samples are sent by users to the facility by express courier and processed by dedicated operators at the HTX lab. Results together with all experimental parameters are made available to users in real time through our web-based CRystallization Information Management System (CRIMS). All samples received are assayed through a specifically developed method that enables to estimate the crystallization likelihood of the sample. Based on the results of this assay specific recommendations are made to users concerning the optimal incubation temperature and possible sample optimisation experiments.

In addition to the standard protocols we have developed specific procedures to handle samples with special requirements like membrane proteins for example. We are also actively involved in the development and evaluation of new technologies in macromolecular crystallization.

The HTX lab can also offer support for structure determination on a collaborative basis.

Publications

CrystalDirect technology: Cipriani & Marquez 2012 Acta Cryst. D68, 1393--1399; Zander et al. (2016) Acta Cryst. D72, 454-466

Methods for sample evaluation and quality control: Dupeux et al., 2011. Acta Cryst. D67,Mariaule et al., 2014Methods in Molecular Biology1091

On the crystallization likelihood of the sample: Dupeux et al., 2011. Acta Cryst. D67

From TNA projects: Malpartida et al. 2017. Nat Comm. 8; Bezerra et al., Sci Rep.  2017.; Wagner et al., 2017. Ange Chem 56.

Services at EMBL Grenoble

EMBL Grenoble provides a number of research services to in-house and external users as well as having access to the services provided by other units of EMBL.