Fast Area Detector Research Articles

The fluctuation-dissipation measurement instrument at the Linac Coherent Light Source.

The development of new modes at x-ray free electron lasers has inspired novel methods for studying fluctuations at different energies and timescales. For closely spaced x-ray pulses that can be varied on ultrafast time scales, we have constructed a pair of advanced instruments to conduct studies targeting quantum materials. We first describe a prototype instrument built to test the proof-of-principle of resonant magnetic scattering using ultrafast pulse pairs. This is followed by a description of a new endstation, the so-called fluctuation-dissipation measurement instrument, which was used to carry out studies with a fast area detector. In addition, we describe various types of diagnostics for single-shot contrast measurements, which can be used to normalize data on a pulse-by-pulse basis and calibrate pulse amplitude ratios, both of which are important for the study of fluctuations in materials. Furthermore, we present some new results using the instrument that demonstrates access to higher momentum resolution.

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest.

Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ, a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples.

Understanding Micromechanical Material Behavior Using Synchrotron X-rays and In Situ Loading

With the flux of high-energy, deeply penetrating X-rays that a 3rd-generation synchrotron source can provide and the current generation of large fast area detectors, the development and use of synchrotron X-ray methods have experienced impressive growth over the past two decades. This paper describes the current state of an important subset of synchrotron methods—high-energy X-ray diffraction employing in situ loading. These methods, which are known by many acronyms such as 3D X-ray diffraction (3DXRD), diffraction contrast tomography (DCT), and high-energy X-ray diffraction microscopy (HEDM), have shifted the focus of alloy characterization to include crystal scale behaviors in addition to microstructure and have made it possible to track the evolution of a polycrystalline aggregate during loading conditions that mimic alloy processing or in-service conditions. The paper is delineated into methods for characterizing elastic behavior including measuring the stress tensor experienced by each crystal and the inelastic response including crystal plasticity, phase transformations, and the onset of damage. We discuss beam size and detector placement, resolution, and speed in the context of the spatial and temporal resolution and scope of the resulting data. Work that emphasizes material models and the interface of data with various numerical simulations and machine learning is presented.

The Extreme Conditions Beamline P02.2 and the Extreme Conditions Science Infrastructure at PETRA III.

A detailed description is presented of the Extreme Conditions Beamline P02.2 for micro X-ray diffraction studies of matter at simultaneous high pressure and high/low temperatures at PETRA III, in Hamburg, Germany. This includes performance of the X-ray optics and instrumental resolution as well as an overview of the different sample environments available for high-pressure studies in the diamond anvil cell. Particularly emphasized are the high-brilliance and high-energy X-ray diffraction capabilities of the beamline in conjunction with the use of fast area detectors to conduct time-resolved compression studies in the millisecond time regime. Finally, the current capability of the Extreme Conditions Science Infrastructure to support high-pressure research at the Extreme Conditions Beamline and other PETRA III beamlines is described.

Real time study of wet-chemical reaction dynamics at beamline P02.1 @ PETRA III

The high brilliance synchrotron light source PETRA III in Hamburg, Germany, provides a dedicated X-ray powder diffraction beamline called P02.1 [1]. It is a side station to the hard X-ray diffraction beamline and runs at a fixed photon energy of 60 keV. Its dispersive monochromator produces a highly collimated photon beam of very narrow energy bandwidth and high intensity. These excellent beam characteristics turn P02.1 into an ideal instrument for many different kinds of experiments, ranging from high resolution powder diffraction of polycrystalline materials for structure solution and refinement or microstructure analysis, to the study of nanocrystalline and disordered materials to determine their local structure. In particular, it is the scope of P02.1 to study dynamic processes such as chemical and crystallographic transitions under non-ambient conditions in real time. For this purpose, the beamline is equipped with a large and fast area detector which enables sub-second time-resolution. The accessible range in reciprocal space is beyond Q = 30 Å-1. Hence, P02.1 is a powerful tool for total scattering experiments as it provides high resolution in real and reciprocal space which are determined by the max. Q and the instrumental resolution, respectively. This presentation describes some recent experiments carried out at P02.1 that relate to pair distribution function (PDF) and total scattering analysis. The focus will be on the investigation of structural changes on the atomic scale during the wet-chemical synthesis of nanoparticles, e.g. in the system ZrO2. By means of evaluating the changes of bond distances and atomic coordination on a time scale of seconds, it is possible to describe the molecular structure of intermediates and, thus, to deduce the underlying reaction mechanism. On the basis of this information, synthesis processes may be optimised with respect to tuning the properties of the product and to maximize its yield.

Structural characterization of the of inorganic and organic hydrotalcites

Layered double hydroxides are versatile materials used for intercalating bioactive molecules, both in pharmaceutical and cosmetic fields, with the purpose of protecting them from degradation, enhancing their water solubility to increase bioavailability, and/or obtaining modified release properties. Hydrotalcite is commercially available in its carbonate form, which is usually transformed into the nitrate form and finally exchanged by organic anions to obtain or regulate bioactivity or photo-activity effects (1). In this study all the steps of these transformations were characterized from the structural viewpoints by X-ray powder diffraction (XRPD) and automated electron diffraction tomography (ADT). ADT allowed shedding light on the nitrate position and conformation inside LDH. XRPD demonstrated at first that the presence of carbonate impurities is able to drive the intercalation of organic molecules into LDH, since CO32- contaminated samples tend to assume d-spacings roughly multiple of LDH-CO3 d-spacing. Finally XRPD was employed at in situ conditions to unravel the structural transformation occurring during the substitution of carbonate by nitrate ion and of the nitrate ion by organic anions. The carbonate-nitrate substitutions resulted to be very rapid (only few seconds) and only the use of a fast area detector, coupled to synchrotron radiation, allowed obtaining reliable patterns to perform XRPD refinement of the disordered structure at the sub-second time resolution. The nitrate-organic substitution resulted slower and depending on the chemical properties of the organic molecules.

Crystal structures of three complexes between chito-oligosaccharides and lysozyme from the rainbow trout. How distorted is the NAG sugar in site D?

Like all c-type lysozymes, those from rainbow trout act as 1,4-beta-acetyl-muramidases to destroy bacteria by cleaving the polysaccharide chains of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) units in the cell walls. Lysozymes also hydrolyse chitin, the analogous N-acetylglucosamine polymer. The rainbow trout enzymes have been shown to be particularly effective in bacterial defence. We have determined the crystal structures of three complexes between rainbow trout lysozyme (RBTL) and the chito-oligosaccharides (NAG)(2), (NAG)(3) and (NAG)(4) to resolutions of 1.8, 2.0 and 1.6 A, respectively. Crystals of these complexes were obtained by co-crystallization, and intensity data were collected on a FAST area detector system. Refinement and model building gave final R values of 16.6, 15.9 and 16.5% for the di-, tri- and tetrasaccharide complexes, respectively. The results show that the chito-oligosaccharides bind to sites A, B and C as previously observed for complexes between the hen egg-white lysozyme (HEWL) and a variety of saccharides. The NAG ring in site D is not bound so deeply and is only slightly distorted towards a half-chair conformation as observed for the equivalent NAM residue in HEWL. From our results, there is reason to question the position and the degree of strain of the D saccharide and the mode of binding and importance of two saccharides in sites E and F for correct orientation of sugar D and effective hydrolysis of a productive substrate-lysozyme complex. Simple model building study from our structures implies a 'left-sided' binding mode of (NAG)(6) in the lower part of the active site of RBTL.

Millisecond molecular events in dynamic biological systems recorded using fast area detectors: current achievements and future needs

Excellent progress is being made in the study of rapid molecular movements in intact biological systems such as muscle using low-angle X-ray diffraction, synchrotron sources and very fast area detectors. However, there is still a need for faster detectors of higher spatial resolution.

Trigonal crystals of porin from Escherichia coli

Trigonal crystals of the integral membrane protein porin from Escherichia coli have been grown and characterized. They belong to space group P321 with unit cell constants a = b = 118.4, c = 52.7 A ̊ , α = β = 90∘, γ = 120∘. The crystals grow as well-defined hexagonal prisms to a size of 0.25 mm in all dimensions, and diffract to 2.7 Å. The molecular symmetry coincides with 3-fold crystallographic symmetry, giving two trimers per unit cell (1 monomer/asymmetric unit). This corresponds to V M = 2.9 A ̊ 3/Da . Native X-ray data to 3.0 Å resolution have been collected on a FAST area detector and a search for heavy atom derivatives is underway.

Engineering enzyme subsite specificity: preparation, kinetic characterization, and x-ray analysis at 2.0-.ANG. resolution of Val111Phe site-mutated calf chymosin

Comparison of the three-dimensional structure of bovine chymosin with the structures of homologous aspartic proteinases complexed with peptide inhibitors shows that Val111 in chymosin occupies a position between the specificity subsites S1 and S3. A mutation corresponding to Val111 to Phe has been introduced in an intermediary plasmid construct of prochymosin by bridging its unique restriction sites by a synthetic mutant oligonucleotide duplex. A prochymosin fusion product was expressed in Escherichia coli in such a way that the extension and substitution of the propart does not interfere with the activation of the zymogen. After activation of the crude prochymosin, the enzyme was purified by affinity chromatography on Sepharose with V-dL-P-F-F-V-dL as ligand. This procedure provided large amounts of pure protein as judged by FPLC, the activity/protein ratio, and SDS-PAGE. The enzymatic properties were determined by using a variety of peptide substrates and inhibitors; KM values for the mutant enzyme were approximately twice those of the wild type, but the kcat values were little changed. The mutant enzyme was crystallized, X-ray data were collected to 2.0-A resolution by using a FAST area detector, and the structure was solved by using difference Fourier methods and refined to an R factor of 19.5%. The mutation leads to only local changes in conformation, with the phenylalanine side chain occupying part of the S1 and S3 pockets. This accounts for the increased KM of this mutant for a substrate with a large phenylalanine side chain at P1. It is also consistent with the higher affinity of the mutant for an inhibitor with small side chains at P1 and P3 when compared with the wild-type enzyme.

ABSCOR: a scaling and absorption correction program for the FAST area detector diffractometer

A Fortran computer program is described which carries out scaling and absorption corrections and a post-correction of the non-uniformity of response of the detector for FAST area detector diffractometer data. The program runs under the VMS operating system.

Combined use of monochromatic and Laue diffraction techniques for macromolecular structure determination.

A novel strategy of macromolecular structure analysis is described which combines the use of monochromatic scanning Laue (SCL) and white-beam Laue (WBL) diffraction techniques. It provides, when applied with an area detector with on-line capabilities, a means of interactively determining and optimizing experimental parameters; it further makes rapid data evaluation feasible, also with off-line detector systems. These new procedures have been applied to a protein structure, beta-trypsin, using a FAST area detector (Enraf-Nonius) and image plates (Fuji) on a double-focusing synchrotron beamline at DORIS. Structure factors, which were derived from FAST Laue data, were empirically scaled by comparing equivalent reflections in different wavelength bins. A 2Fo-Fc difference Fourier map, which was calculated at 1.8 A resolution using these structure-factor moduli together with phases from the known structural model, showed well defined electron density distribution (R = 22%). Image-plate exposures showed diffraction to 1.2 A resolution. The effect of crystal mosaicity on the maximum wavelength bandwidth for Laue exposures has been investigated. SCL techniques, which involve rapid scanning (with a crystal or multilayer monochromator or a tunable undulator) through a defined wavelength range, extend the applicability of Laue techniques to crystals with broadened mosaic spread.

Piperazine silicate (EU 19): the structure of a very small crystal determined with synchrotron radiation

Single-crystal diffraction data have been recorded for a very small crystal of dimensions 8 x 18 × 175 ~rn 3. From these data the structure of piperazine silicate (EU 19) has been determined and refined to R = 0.094 for 490 observed reflections. Data collection for such a crystal has been made practicable by the high intensity of the Daresbury Synchrotron Radiation Source and the Enraf-Nonius FAST area detector diffractometer. The potential of this synchrotron radiation method for other small crystals including proteins is discussed. Crystal data: 2+ • 2

Crystallization, crystal structure analysis and preliminary molecular model of the bilin binding protein from the insect Pieris brassicae

The bilin binding protein of the butterfly Pieris brassicae has been prepared, crystallized and its crystal structure determined at high resolution using film and FAST area detector intensity data. The crystallographic asymmetric unit contains a tetramer of identical subunits with a molecular weight of about 90,000. The crystal structure was determined by isomorphous replacement. Use was made of the molecular symmetry to improve phases. A molecular interpretation of the electron density distribution and partial tracing of the polypeptide chain was possible without amino acid sequence information, as the fold is very similar to retinol binding protein. It is characterized by a β-barrel formed by two orthogonal β-sheets and an α-helix. The bilin pigment seems to be bound within the β-barrel analogously to retinol in retinol binding protein. The tetramer in the crystal has C2 symmetry and is a dimer of dimers of quasi-equivalent subunits.