The production of three-dimensional crystallographic structural information of macromolecules can now be thought of as a pipeline that is being streamlined at every stage from protein cloning, expression and purification, through crystallisation to data collection and structure solution. Synchrotron X-ray beamlines are a key section of this pipeline as they are where the X-ray diffraction data are collected, which ultimately leads to the elucidation of macromolecular structures. The throughput of macromolecular crystallography (MX) beamlines may be enhanced significantly with the automation of both their operation and of the experiments carried out [1].

Any automation procedure should include all of the steps shown in Figure 83: provision of a suitable X-ray beam onto the sample, the mounting, dismounting and storage of the sample, reduction (integration and scaling) of any data collected, initial structure solution and refinement processes and the linking of synchrotron radiation macromolecular crystallography (SRMX) experiments with home laboratory information management systems. The automation of SRMX facilities can thus be split neatly into two different aspects: those which the user sees and feels directly such as robotic sample changers and information management software, and those hidden from view such as automatic beamline validation and alignment routines. Both aspects are being addressed at the ESRF.



Fig. 83: A typical MX experiment. Each step may be automated and the steps must be linked for a fully automatic experiment.


Protocols and software for the automatic alignment of the optical elements of a SRMX facility are essential to ensure its smooth and efficient operation. Automatic beamline alignment (ABA) procedures to achieve this and a historical database that allows monitoring and correction of the optical element positions have been developed. The ABA routines currently implemented or under development on the MX beamlines include calibrating, selecting and maintaining the X-ray energy, focussing the X-ray beam onto the sample position [2] and maintaining the integrity of the X-ray beam by monitoring its position and intensity using X-ray beam position monitors (XBPMs). For efficient automated beamline alignment, it is essential that the position and status of all beamline elements are monitored, stored and compared with those corresponding to an optimum alignment of the beamline. Any significant deviation from this ideal configuration should then trigger a re-alignment of the beamline. At the ESRF, a historical database has been modelled on the comprehensive database that is used in tracking the performance of the storage ring.

The high throughput demanded of today's MX beamlines can only be accomplished by the integration of an automatic sample changer as a beamline component. When installing a sample changer on the beamline one has to consider the automation of all aspects of a MX data collection experiment in order to maximise the benefit from the device:

  • Sample identification, tracking and the handling of sample information known before an experiment commences, should allow automatic beamline preparation.
  • Characterisation of each sample held in the sample changer (including the determination of unit cell dimensions, Laue Group, orientation matrix and data collection strategy).
  • Scoring and ranking of the samples contained in the sample changer and the collection and processing of diffraction data.
  • Feedback, where intermediate results suggest strategic modifications to the on-going data collection should also be possible.
  • Sample and information tracking inevitably involves the use of databases.

The EMBL Grenoble Outstation and the ESRF have developed sample changer robots that can hold up to 50 frozen samples. They will be installed on all ESRF MX beamlines by the end of 2005. The DNA software [3] for automatic crystal characterisation, determination of optimal data collection parameters and the processing of diffraction data is already available on all MX beamlines. The beamline experiment database (PXWeb/ISpyB) allows the submission and tracking of sample information and the exchange of data between the ESRF and the user home laboratory. Extensive tests of this data exchange pipeline are currently ongoing.

The sample changer robots are compatible with the mini- and micro-diffractometers that have been installed on nearly all of the MX beamlines (ID14-2,-3,-4, ID23-1, ID29). These diffractometers incorporate on-beam-axis visualisation of the sample, a high-precision air-bearing phi spindle and automatic sample centring and sample-to-beam alignment capabilities. A motorised mini-kappa system is under development as an add-on for the diffractometer.



Fig. 84: The current status of automation at the MX beamlines. Each automated step is controlled via different software interfaces.


The automation effort on the MX beamlines is continuously advancing and the links between each individual module of the MX experiment becoming seamless (Figure 84). This push towards increased automation will provide an efficient and effective environment for high-throughput MX.

[1] S. Arzt et al, Prog. Biophys. Mol. Biol. in press.
[2] O. Hignette et al, X-Ray Micro- and Nano-Focusing: Applications and Techniques II, Proceedings of SPIE, 4499 105-116 (2001).

J. McCarthy on behalf of the Joint Structural Biology Group (JSBG) of the ESRF and the EMBL Grenoble Outstation.