To automate or not to automate: this is the question

Abstract

New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected.

Fig. 1

A schematic overview of the LabDB system. The four components of the system are shown connected by solid arrows, while laboratory systems from which data are automatically extracted are shown connected by dotted lines

Fig. 2

A Number of data sets collected and structures deposited for beamline 5.0.2 at ALS. The green arrow indicates the introduction of an automatic crystal mounting system. B Number of datasets collected and structures deposited for beamline X4A at NSLS. The green arrow indicates introduction of an automatic image plate detector, and the purple line marks introduction of a CCD detector

Fig. 3

Application of the ligand analysis module in HKL-3000 to the study of ligand binding properties of APC7551, a universal stress protein from Archaeoglobus fulgidus. A The module interface that describes the soak composition. B The bound component of the soak cocktail, CDP, is automatically fit into the additional electron density (2F _o − F _c is blue, F _o − F _c is green). C A fit of an incorrect component of the soak cocktail, trehalose, into the same density. D A scoring diagram that describes the fit of the soak components into electron density (CDP is number 5, trehalose is number 9)

Fig. 4

Distributions of Zn-to-water-oxygen distances in the Cambridge Structural Database (CSD, red), a set of high resolution PDB structures (<1.5 Å), and a set of medium resolution PDB structures (2.0–2.5 Å)

Fig. 5

The water molecule validation window in HKL-3000. A The original distribution of water oxygen atoms by B-factor in PDB deposit 3EME. B The distribution of water oxygen atoms by B-factor after structure rerefinement

Fig. 6

Rerefinement of PDB structure 3BQS. A Electron density and model of 3BQS as reported in the PDB. B The same electron density region after re-refinement with HKL-3000 and redeposition as 3MAB