Accurate and highly complete synchrotron protein crystal Laue diffraction data using the ESRF CCD and the Daresbury Laue software

Abstract

Developments in electronic area detectors such as CCDs and image plates have transformed the capability of the synchrotron Laue protein crystallography technique compared with film. The rapid readout of CCDs makes practical the use of rather fine angular interval settings of the crystal between each Laue exposure and a large overall angle coverage. The use of the ESRF CCD (image intensifier type) presented here in the Laue data collection on ESRF ID09 (the `Laue beamline') from a single crystal of the 34 kDa wild‐type hydroxymethylbilane synthase (HMBS), space group P21212 a = 88.06, b = 75.73, c = 50.35 Å, yielded 47 Laue exposures in 2.5° angle intervals from a single crystal. The data processed by the Daresbury Laue software is highly complete (∞–2dmin = 77.5%; 2dmin–dmin= 91.7%) to 2.3 Å with high redundancy (11.2). Comparison with calculated structure factors and careful analysis of the Laue geometry shows that between ∞ and 5dmin better completeness still should be possible, which can ideally be realized from CCD detector dynamic range hardware improvements and/or software algorithms to integrate saturated spot profiles. Prospects for Laue diffraction data collection using yet faster detectors such as the `pixel detector' to study irreversible catalytic structural processes in a crystal, the most challenging of all time‐resolved experiments, are bright.

Extraction of accurate structure-factor amplitudes from Laue data: wavelength normalization with wiggler and undulator X-ray sources

“…Advances in Laue data processing during the last decade (Campbell & Hao, 1993;Ren & Moffat, 1995a,b;Bourenkov et al, 1996;Bourgeois et al, 1998;Clifton et al, 1997) addressed and resolved the energy and spatial overlap problems, traditionally considered problems serious enough to limit the use of the technique. This signi®cantly improved the quality and completeness of Laue data collected using more standard broad-bandpass sources such as bending magnets and wigglers, and led to a wider use of the Laue technique (Ren & Moffat, 1995a,b;Perman et al, 1998;Yang et al, 1998;Ravelli et al, 1999;Nieh et al, 1999;Ren et al, 1999). Sources with a relatively narrow spectral bandpass, such as single-line undulators, reduce harmonic and spatial overlaps as well as the polychromatic background in typically crowded Laue patterns (Moffat et al, 1984;Bartunik & Borchert, 1989; Bartunik et al, 1992;Moffat, 1997;Ren et al, 1999).…”

Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane

“…Five crystal structures of E. coli PBGD ( EcPBGD): 1GTK [9] , 1YPN [10] , 2YPN [11] , 1AH5 [12] , 1PDA [8] ; two of hPBGD: 3ECR [13] , 3EQ1 [5] ; and most recently, one of Arabidopsis thaliana PBGD (AtPBGD): 4HTG [14] are available in the protein data bank (PDB) [15] . The structure of EcPBGD ( Figure 2A ) consists of 3 domains of α/β class.…”

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase fromBacillus megaterium

“…The X-ray structure of the Arabidopsis thaliana enzyme has recently been solved (PDB entry 4htg; Roberts et al, 2013); prior to this, structures were available for Escherichia coli PBGD [PDB entries 1pda (Louie et al, 1992(Louie et al, , 1996, 1gtk (Helliwell et al, 2003), 1ah5 (Hä dener et al, 1999, 1ypn (Helliwell et al, 1998) and 2ypn (Nieh et al, 1999)] and the human enzyme (PDB entries 3eq1 and 3ecr; Gill et al, 2009;Song et al, 2009). The polypeptide is folded into three domains (1-3), each of approximately the same size.…”