The PILATUS 1M detector

SynchWeb: a modern interface for ISPyB

SynchWeb is a modern interface to the ISPyB database. It significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography. It adds a variety of new features including project management, an integrated diffraction image viewer, and a map and model viewer, as well as displaying results from automated analysis pipelines. Virtually all aspects of an experiment can be monitored through the web browser and the success of each experiment can be evaluated.

Structure determination of an integral membrane protein at room temperature from crystals in situ

The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.

Nanoparticle characterization by means of scanning free grazing emission X-ray fluorescence

Nanoparticles are considered for applications in domains as various as medical and pharmaceutical sciences, opto- and microelectronics, catalysis, photovoltaics, spintronics or nano- and biotechnology. The applications realized with nanocrystals depend strongly on the physical dimensions (shape and size) and elemental constitution. We demonstrate here that grazing emission X-ray fluorescence (GEXRF) is an element sensitive technique that presents the potential for a reliable and accurate determination of the morphology of nanoparticles deposited on a flat substrate (ready-to-use devices). Thanks to the scanning-free approach of the used GEXRF setup, the composition, shape and average size of nanoparticles are determined in short time intervals, minimizing the exposure to radiation. The (scanning-free) GEXRF technique allows for in situ investigations of the nanoparticulate systems thanks to the penetration properties of both the probe X-ray beam and the emitted X-ray fluorescence signal.

Bunch mode specific rate corrections for PILATUS3 detectors

PILATUS X-ray detectors are in operation at many synchrotron beamlines around the world. This article reports on the characterization of the new PILATUS3 detector generation at high count rates. As for all counting detectors, the measured intensities have to be corrected for the dead-time of the counting mechanism at high photon fluxes. The large number of different bunch modes at these synchrotrons as well as the wide range of detector settings presents a challenge for providing accurate corrections. To avoid the intricate measurement of the count rate behaviour for every bunch mode, a Monte Carlo simulation of the counting mechanism has been implemented, which is able to predict the corrections for arbitrary bunch modes and a wide range of detector settings. This article compares the simulated results with experimental data acquired at different synchrotrons. It is found that the usage of bunch mode specific corrections based on this simulation improves the accuracy of the measured intensities by up to 40% for high photon rates and highly structured bunch modes. For less structured bunch modes, the instant retrigger technology of PILATUS3 detectors substantially reduces the dependency of the rate correction on the bunch mode. The acquired data also demonstrate that the instant retrigger technology allows for data acquisition up to 15 million photons per second per pixel.

Real-space evidence of the equilibrium ordered bicontinuous double diamond structure of a diblock copolymer

The ordered bicontinuous double diamond (OBDD) structure has long been believed to be an unstable ordered network nanostructure, which is relative to the ordered bicontinuous double gyroid (OBDG) structure for diblock copolymers. Using electron tomography, we present the first real-space observation of the thermodynamically stable OBDD structure in a diblock copolymer composed of a stereoregular block, syndiotactic polypropylene-block-polystyrene (sPP-b-PS), in which the sPP tetrapods are interconnected via a bicontinuous network with Pn3̄m symmetry. The OBDD structure underwent a thermally reversible order-order transition (OOT) to OBDG upon heating, and the transition was accompanied with a slight reduction of domain spacing, as demonstrated both experimentally and theoretically. The thermodynamic stability of the OBDD structure was attributed to the ability of the configurationally regular sPP block to form helical segments, even above its melting point, as the reduction of internal energy associated with the helix formation may effectively compensate the greater packing frustration in OBDD relative to that in the tripods of OBDG.

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.

X-ray structure of the pestivirus NS3 helicase and its conformation in solution

Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication.

IMPORTANCE

Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the unwinding specificity of pNS3h, which is active only on RNA duplexes. We also show that pNS3h has a highly dynamic behavior--a characteristic probably shared with NS3 helicases from all Flaviviridae members--that could be targeted for drug design by using recent algorithms to specifically block molecular motion. Compounds that lock the enzyme in a single conformation or limit its dynamic range of conformations are indeed likely to block its helicase function.

Application of in situ diffraction in high-throughput structure determination platforms

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

High-throughput studies of protein shapes and interactions by synchrotron small-angle X-ray scattering

Solution-based small angle X-ray scattering (SAXS) affords the opportunity to extract accurate structural parameters and global shape information from diverse biological macromolecular systems. SAXS is an ideal complementary technique to other structural and biophysical methods but it can also be applied alone to access structural information that is otherwise unobtainable using high-resolution methods. Macromolecular structures ranging from kilodaltons to gigadaltons can be analyzed, which encompasses the size of most proteins and functional cellular complexes. The SAXS analysis is performed using only a few microliters of solution containing microgram quantities of purified material in sample environments that can be tailored to mimic physiological conditions or altered to suit a particular question. High-brilliance synchrotron X-ray sources and parallel advances in hardware and computing have reduced data acquisition times to the millisecond range and the application of automated methods have allowed data processing and low resolution shape modelling to be completed within minutes. These developments have paved the way for high-throughput studies that generate significant quantities of structural information over a short period of time. Here, we briefly consider the basics of SAXS and describe major methods and protocols employed in high-throughput SAXS studies.

Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments

Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.

Diffuse scattering and partial disorder in complex structures

The study of single-crystal diffuse scattering (SCDS) goes back almost to the beginnings of X-ray crystallography. Because SCDS arises from two-body correlations, it contains information about local (short-range) ordering in the sample, information which is often crucial in the attempt to relate structure to function. This review discusses the state of the field, including detectors and data collection and the modelling of SCDS using Monte Carlo and ab initio techniques. High-quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing ever more detailed and quantitative analyses to be undertaken, and opening the way to approaches such as three-dimensional pair distribution function studies (3D-PDF) and automated refinement of a disorder model, powerful techniques that require large volumes of low-noise data.

Time-resolved crystallography using the Hadamard transform

We describe a method for performing time-resolved X-ray crystallographic experiments based on the Hadamard transform, in which time resolution is defined by the underlying periodicity of the probe pulse sequence, and signal/noise is greatly improved over that for the fastest pump-probe experiments depending on a single pulse. This approach should be applicable on standard synchrotron beamlines and will enable high-resolution measurements of protein and small-molecule structural dynamics. It is also applicable to other time-resolved measurements where a probe can be encoded, such as pump-probe spectroscopy.

A new spectrometer design for the x-ray spectroscopy of laser-produced plasmas with high (sub-ns) time resolution

This paper describes a new type of x-ray crystal spectrometer, which can be used in combination with gated x-ray detectors to obtain spectra from laser-produced plasmas with a high (sub-ns) time resolution. The spectrometer consists of a convex, spherically bent crystal, which images individual spectral lines as perfectly straight lines across multiple, sequentially gated, strip detectors. Since the Bragg-reflected rays are divergent, the distance between detector and crystal is arbitrary, so that this distance can be appropriately chosen to optimize the experimental arrangement with respect to the detector parameters. The spectrometer concept was verified in proof-of-principle experiments by imaging the Lβ1- and Lβ2-lines of tungsten, at 9.6735 and 9.96150 keV, from a micro-focus x-ray tube with a tungsten target onto a two-dimensional pixilated Pilatus detector, using a convex, spherically bent Si-422 crystal with a radius of curvature of 500 mm.

Contributions of charge-density research to medicinal chemistry

This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.

Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering

We used small-angle X-ray scattering (SAXS) to evaluate the solution structure of a double-stranded RNA with 32 base pairs. We wanted to compare the solution structure to the crystal structure to assess the impact of the crystal lattice on the overall conformation of the RNA. The RNA was designed to self-anneal and form a head-to-head fusion of two identical mRNA/oligo(U) tail domains (the U-helix) from a trypanosome RNA editing substrate formed by the annealing of a guide RNA to a pre-edited mRNA. This substrate is from the U insertion/deletion RNA editing system of trypanosomes. Each strand in the fusion RNA had 16 purines from the pre-mRNA followed by 16 uracils (Us) from the U-tail at the 3' end of the guide RNA. The strands were designed to form a double helix with blunt ends, but each strand had the potential to form hairpins and single-stranded RNA helices. Hairpins could form by the 3' oligouridylate tract folding back to hybridize with the 5' oligopurine tract and forming an intervening loop. Single-stranded helices could form by the stacking of bases in the polypurine tract. Some of the 16 Us 3' to the polypurine tract may have been unstacked and in random coils. Our SAXS studies showed that the RNA formed a mix of single-stranded structures in the absence of MgCl2. In the presence of MgCl2 at concentrations similar to those in the crystal, the solution structure was consistent with the double-stranded, blunt-ended structure, in agreement with the crystal structure. Here we describe the preparation of RNA samples, data collection with an in-house SAXS instrument designed for biological samples, and the processing and modeling of the scattering data.

First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate

The aim of this study was to test the applicability of a Bruker AXS CMOS-type PHOTON 100 detector for the purpose of a fine charge density quality data collection. A complex crystal containing oxalic acid, ammonium oxalate and two water molecules was chosen as a test case. The data was collected up to a resolution of 1.31 Å−1with high completeness (89.1%;Rmrg= 0.0274). The multipolar refinement and subsequent quantum theory of atoms in molecules (QTAIM) analysis resulted in a comprehensive description of the charge density distribution in the crystal studied. The residual density maps are flat and almost featureless. It was possible to derive reliable information on intermolecular interactions to model the anharmonic motion of a water molecule, and also to observe the fine details of the charge density distribution, such as polarization on O and H atoms involved in the strongest hydrogen bonds. When compared with our previous statistical study on oxalic acid data collected with the aid of CCD cameras, the complementary metal-oxide semiconductor (CMOS) detector can certainly be classified as a promising alternative in advanced X-ray diffraction studies.

An optical chopper for generation of short X-ray pulses to allow in-house time-resolved photocrystallography

As part of a project to implement in-house time-resolved diffraction of short-lifetime species, a fast shutter with a custom-designed enclosure has been installed. The device is suitable for generation of X-ray pulses with time lengths down to about 5 µs. The design does not require major modifications to commercially available diffractometer setups. Significant airflow, generated by the rotating chopper disc, which interferes with temperature control at the sample, has been eliminated by a compact enclosure, which does not interfere with sample monitoring and conditioning devices. It allows for full rotation of the diffractometer circles.

Contemporary X-ray electron-density studies using synchrotron radiation

Synchrotron radiation has many compelling advantages over conventional radiation sources in the measurement of accurate Bragg diffraction data. The variable photon energy and much higher flux may help to minimize critical systematic effects such as absorption, extinction and anomalous scattering. Based on a survey of selected published results from the last decade, the benefits of using synchrotron radiation in the determination of X-ray electron densities are discussed, and possible future directions of this field are examined.

High-dynamic-range coherent diffractive imaging: ptychography using the mixed-mode pixel array detector

Coherent (X-ray) diffractive imaging (CDI) is an increasingly popular form of X-ray microscopy, mainly due to its potential to produce high-resolution images and the lack of an objective lens between the sample and its corresponding imaging detector. One challenge, however, is that very high dynamic range diffraction data must be collected to produce both quantitative and high-resolution images. In this work, hard X-ray ptychographic coherent diffractive imaging has been performed at the P10 beamline of the PETRA III synchrotron to demonstrate the potential of a very wide dynamic range imaging X-ray detector (the Mixed-Mode Pixel Array Detector, or MM-PAD). The detector is capable of single photon detection, detecting fluxes exceeding 1 × 10(8) 8-keV photons pixel(-1) s(-1), and framing at 1 kHz. A ptychographic reconstruction was performed using a peak focal intensity on the order of 1 × 10(10) photons µm(-2) s(-1) within an area of approximately 325 nm × 603 nm. This was done without need of a beam stop and with a very modest attenuation, while `still' images of the empty beam far-field intensity were recorded without any attenuation. The treatment of the detector frames and CDI methodology for reconstruction of non-sensitive detector regions, partially also extending the active detector area, are described.

A high pressure cell for supercritical CO₂ on-line chemical reactions studied with X-ray techniques

A versatile high pressure X-ray sample cell has been developed for conducting in situ time-resolved X-ray scattering experiments in the pressure and temperature regime required (pressures up to 210 bars and temperatures up to 120 °C) for chemical reactions in supercritical fluids. The large exit opening angle of the cell allows simultaneous performance of SAXS-WAXS experiments. Diamond windows are used in order to benefit from the combination of maximum strength, minimal X-ray absorption and chemical inertia. The sample cell can also be utilised for X-ray spectroscopy experiments over a wide range of photon energies. Results of the online synthesis of a block copolymer, poly(methyl methacrylate-block-poly(benzyl methacrylate), by Reversible Addition-Fragmentation Chain Transfer (RAFT) in a supercritical CO2 dispersion polymerisation will be discussed. The contribution of the density fluctuations, as function of temperature, to the X-ray scattering signal has been quantified in order to allow appropriate background subtractions.

Linear fitting of multi-threshold counting data with a pixel-array detector for spectral X-ray imaging

Experiments and modeling are described to perform spectral fitting of multi-threshold counting measurements on a pixel-array detector. An analytical model was developed for describing the probability density function of detected voltage in X-ray photon-counting arrays, utilizing fractional photon counting to account for edge/corner effects from voltage plumes that spread across multiple pixels. Each pixel was mathematically calibrated by fitting the detected voltage distributions to the model at both 13.5 keV and 15.0 keV X-ray energies. The model and established pixel responses were then exploited to statistically recover images of X-ray intensity as a function of X-ray energy in a simulated multi-wavelength and multi-counting threshold experiment.

The crystal structure of ferritin from Chlorobium tepidum reveals a new conformation of the 4-fold channel for this protein family

Ferritins are ubiquitous iron-storage proteins found in all kingdoms of life. They share a common architecture made of 24 subunits of five α-helices. The recombinant Chlorobium tepidum ferritin (rCtFtn) is a structurally interesting protein since sequence alignments with other ferritins show that this protein has a significantly extended C-terminus, which possesses 12 histidine residues as well as several aspartate and glutamic acid residues that are potential metal ion binding residues. We show that the macromolecular assembly of rCtFtn exhibits a cage-like hollow shell consisting of 24 monomers that are related by 4-3-2 symmetry; similar to the assembly of other ferritins. In all ferritins of known structure the short fifth α-helix adopts an acute angle with respect to the four-helix bundle. However, the crystal structure of the rCtFtn presented here shows that this helix adopts a new conformation defining a new assembly of the 4-fold channel of rCtFtn. This conformation allows the arrangement of the C-terminal region into the inner cavity of the protein shell. Furthermore, two Fe(III) ions were found in each ferroxidase center of rCtFtn, with an average FeA-FeB distance of 3 Å; corresponding to a diferric μ-oxo/hydroxo species. This is the first ferritin crystal structure with an isolated di-iron center in an iron-storage ferritin. The crystal structure of rCtFtn and the biochemical results presented here, suggests that rCtFtn presents similar biochemical properties reported for other members of this protein family albeit with distinct structural plasticity.

Characterization of an in-vacuum PILATUS 1M detector

A dedicated in-vacuum X-ray detector based on the hybrid pixel PILATUS 1M detector has been installed at the four-crystal monochromator beamline of the PTB at the electron storage ring BESSY II in Berlin, Germany. Owing to its windowless operation, the detector can be used in the entire photon energy range of the beamline from 10 keV down to 1.75 keV for small-angle X-ray scattering (SAXS) experiments and anomalous SAXS at absorption edges of light elements. The radiometric and geometric properties of the detector such as quantum efficiency, pixel pitch and module alignment have been determined with low uncertainties. The first grazing-incidence SAXS results demonstrate the superior resolution in momentum transfer achievable at low photon energies.

Co-crystallization with conformation-specific designed ankyrin repeat proteins explains the conformational flexibility of BCL-W

BCL-W is a member of the BCL-2 family of anti-apoptotic proteins. A key event in the regulation of apoptosis is the heterodimerization between anti-apoptotic and pro-apoptotic family members, which involves a conserved surface-exposed groove on the anti-apoptotic proteins. Crystal structures of the ligand binding-competent conformation exist for all anti-apoptotic family members, with the exception of BCL-W, due to the flexibility of the BCL-W groove region. Existing structures had suggested major deviations of the BCL-W groove region from the otherwise structurally highly related remaining anti-apoptotic family members. To capture its ligand binding-competent conformation by counteracting the conformational flexibility of the BCL-W groove, we had selected high-affinity groove-binding designed ankyrin repeat proteins (DARPins) using ribosome display. We now determined two high-resolution crystal structures of human BCL-W in complex with different DARPins at resolutions 1.5 and 1.85Å, in which the structure of BCL-W is virtually identical, and BCL-W adopts a conformation extremely similar to the ligand-free conformation of its closest relative BCL-XL in both structures. However, distinct differences to all previous BCL-W structures are evident, notably in the ligand-binding region. We provide the first structural explanation for the conformational flexibility of the BCL-W groove region in comparison to other BCL-2 family members. Due to the importance of the anti-apoptotic BCL-2 family as drug targets, the presented crystal structure of ligand binding-competent BCL-W may serve as a valuable basis for structure-based drug design in the future and provides a missing piece for the structural characterization of this protein family.

From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display

Antibodies are the most versatile binding proteins in nature with six loops creating a flexible continuous interaction surface. However, in some molecular formats, antibodies are aggregation prone. Designed ankyrin repeat proteins (DARPins) were successfully created as alternative design solutions. Nevertheless, their concave shape, rigidity and incompletely randomized binding surface may limit the epitopes that can be targeted by this extremely stable scaffold. Combining conformational diversity and a continuous convex paratope found in many antibodies with the beneficial biophysical properties of DARPins, we created LoopDARPins, a next generation of DARPins with extended epitope binding properties. We employed X-ray structure determination of a LoopDARPin for design validation. Biophysical characterizations show that the introduction of an elongated loop through consensus design does not decrease the stability of the scaffold,consistent with molecular dynamics simulations. Ribosome-display selections against extracellular signal-regulated kinase 2 (ERK2) and four members of the BCL-2 family (BCL-2, BCL-XL, BCL-W and MCL-1) of anti-apoptotic regulators yielded LoopDARPins with affinities in the mid-picomolar to low nanomol arrange against all targets. The BCL-2 family binders block the interaction with their natural interaction partner and will be valuable reagents to test the apoptotic response in functional assays. With the LoopDARPin scaffold, binders for BCL-2 with an affinity of 30 pM were isolated with only a single round of ribosome display,an enrichment that has not been described for any scaffold. Identical stringent one-round selections with conventional DARPins without loop yielded no binders. The LoopDARPin scaffold may become a highly valuable tool for biotechnological high-throughput applications.

Developments in x-ray crystallographic structure determination of biological macromolecules

The three-dimensional structures of large biomolecules important in the function and mechanistic pathways of all living systems and viruses can be determined by x-ray diffraction from crystals of these molecules and their complexes. This area of crystallography is continually expanding and evolving, and the introduction of new methods that use the latest technology is allowing the elucidation of ever larger and more complex biological systems, which are now becoming tractable to structure solution. This review looks back at what has been achieved and forward at how current and future developments may allow technical challenges to be overcome.

Approaches to automated protein crystal harvesting

The harvesting of protein crystals is almost always a necessary step in the determination of a protein structure using X-ray crystallographic techniques. However, protein crystals are usually fragile and susceptible to damage during the harvesting process. For this reason, protein crystal harvesting is the single step that remains entirely dependent on skilled human intervention. Automation has been implemented in the majority of other stages of the structure-determination pipeline, including cloning, expression, purification, crystallization and data collection. The gap in automation between crystallization and data collection results in a bottleneck in throughput and presents unfortunate opportunities for crystal damage. Several automated protein crystal harvesting systems have been developed, including systems utilizing microcapillaries, microtools, microgrippers, acoustic droplet ejection and optical traps. However, these systems have yet to be commonly deployed in the majority of crystallography laboratories owing to a variety of technical and cost-related issues. Automation of protein crystal harvesting remains essential for harnessing the full benefits of fourth-generation synchrotrons, free-electron lasers and microfocus beamlines. Furthermore, automation of protein crystal harvesting offers several benefits when compared with traditional manual approaches, including the ability to harvest microcrystals, improved flash-cooling procedures and increased throughput.

X-ray irradiation induced reduction and nanoclustering of lead in borosilicate glass

Under the influence of X-rays an unexpected formation of pure Pb nanoparticles was observed in PbS-doped borosilicate glass.

Automating crystallographic structure solution and refinement of protein-ligand complexes

High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.

Membrane protein structure determination - the next generation

The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.

Screening Ligands by X-ray crystallography

X-ray crystallography is an invaluable technique in structure-based drug discovery, including fragment-based drug discovery, because it is the only technique that can provide a complete three dimensional readout of the interaction between the small molecule and its macromolecular target. X-ray diffraction (XRD) techniques can be employed as the sole method for conducting a screen of a fragment library, or it can be employed as the final technique in a screening campaign to confirm putative "hit" compounds identified by a variety of biochemical and/or biophysical screening techniques. Both approaches require an efficient technique to prepare dozens to hundreds of crystals for data collection, and a reproducible way to deliver ligands to the crystal. Here, a general method for screening cocktails of fragments is described. In cases where X-ray crystallography is employed as a method to verify putative hits, the cocktails of fragments described below would simply be replaced with single fragment solutions.

Measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies

The advent of micro-focused X-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. In particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. However, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be performed. For the automation of this process for large-scale screening, and to provide an indication of the best strategy for data collection, a metric of crystal variability could be useful. Here, measures of the intrinsic variability within protein crystals are presented and their implications for optimal data-collection strategies are discussed.

Scanning-free grazing emission x-ray fluorescence by means of an angular dispersive arrangement with a two-dimensional position-sensitive area detector

We report on the application of a two-dimensional position-sensitive area detector towards grazing emission x-ray fluorescence (GEXRF) spectroscopy. GEXRF allows for surface-sensitive studies with nanometer-scale accuracy in the depth direction by measuring the intensity variation of an x-ray fluorescence line with the grazing emission angle. The presented experimental setup is based on a fixed sample-detector arrangement and does not require any moving components. We show that the dispersion of the grazing emission angle along a position-sensitive detector allows to acquire with an excellent angular resolution a full GEXRF profile in a single measurement. Moreover, the use of a two-dimensional detector allows to perform experiments with an increased solid angle of detection per emission angle. This results in combination with the nonsequential and simultaneous acquisition of the GEXRF profiles of different emission lines in considerably reduced acquisition times. The realization, the demands, and the main characteristics of the scanning-free GEXRF setup will be presented. A few experimental examples will serve to illustrate the analytical possibilities offered by the presented setup.

Structure of human mitochondrial RNA polymerase elongation complex

The crystal structure of the human mitochondrial RNA polymerase (mtRNAP) transcription elongation complex was determined at 2.65 Å resolution. The structure reveals a 9–base pair hybrid formed between the DNA template and the RNA transcript and one turn of DNA both upstream and downstream of the hybrid. Comparisons with the distantly related RNAP from bacteriophage T7 indicates conserved mechanisms for substrate binding and nucleotide incorporation, but also strong mechanistic differences. Whereas T7 RNAP refolds during the transition from initiation to elongation, mtRNAP adopts an intermediary conformation that is capable of elongation without refolding. The intercalating hairpin that melts DNA during T7 RNAP initiation separates RNA from DNA during mtRNAP elongation. Newly synthesized RNA exits towards the PPR domain, a unique feature of mtRNAP with conserved RNA recognition motifs.

A prototype direct-detection CCD for protein crystallography

The fabrication and testing of a prototype deep-depletion direct-conversion X-ray CCD detector are described. The device is fabricated on 600 µm-thick high-resistivity silicon, with 24 × 24 µm pixels in a 4k × 4k pixel format. Calibration measurements and the results of initial protein crystallography experiments at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline are described, as well as suggested improvements for future versions of the detector.

Architecturally diverse proteins converge on an analogous mechanism to inactivate Uracil-DNA glycosylase

Uracil-DNA glycosylase (UDG) compromises the replication strategies of diverse viruses from unrelated lineages. Virally encoded proteins therefore exist to limit, inhibit or target UDG activity for proteolysis. Viral proteins targeting UDG, such as the bacteriophage proteins ugi, and p56, and the HIV-1 protein Vpr, share no sequence similarity, and are not structurally homologous. Such diversity has hindered identification of known or expected UDG-inhibitory activities in other genomes. The structural basis for UDG inhibition by ugi is well characterized; yet, paradoxically, the structure of the unbound p56 protein is enigmatically unrevealing of its mechanism. To resolve this conundrum, we determined the structure of a p56 dimer bound to UDG. A helix from one of the subunits of p56 occupies the UDG DNA-binding cleft, whereas the dimer interface forms a hydrophobic box to trap a mechanistically important UDG residue. Surprisingly, these p56 inhibitory elements are unexpectedly analogous to features used by ugi despite profound architectural disparity. Contacts from B-DNA to UDG are mimicked by residues of the p56 helix, echoing the role of ugi's inhibitory beta strand. Using mutagenesis, we propose that DNA mimicry by p56 is a targeting and specificity mechanism supporting tight inhibition via hydrophobic sequestration.

Diffraction studies under in situ electric field using a large-area hybrid pixel XPAD detector

A new experimental approach to perform in situ electric field diffraction on single crystals using an on-then-off pump–probe mode in situ (i.e. the field-switching method) with a synchrotron or a laboratory X-ray source is presented. Taking advantage of the fast readout of the XPAD hybrid pixel two-dimensional detector and its programmable functionalities, the operation mode of the detector has been customized to significantly increase the efficiency of the method. The very weak electric field-induced structural response of a piezoelectric crystal can be accurately measured. This allows the piezoelectric tensor to be precisely obtained from Δθ shifts while the structural variations can be modelled using a full set of ΔI/I data. The experimental method and methodology are detailed and tested as a case study on pure piezoelectric compounds belonging to the α-quartz family (SiO2 and GaAsO4 single crystals). Using the two scan modes developed, it is demonstrated that tiny Bragg angle shifts can be measured as well as small field-induced Bragg intensity variations (<1%). The relevance of measurements performed with an X-ray laboratory source is demonstrated: partial data sets collected at synchrotrons can be completed, but more interestingly, a large part of the study can now be realized in the laboratory (medium to strong intensity reflections) in a comparable data collection time.

An accidental visualization of the Brillouin zone in an Ni–W alloyviadiffuse scattering

Solid state physics is built on the concept of reciprocal space. The physics of any given periodic crystal is fully defined within the Wigner–Seitz cell in reciprocal space, also known as the first Brillouin zone. It is a purely symmetry-based concept and usually does not have any eye-catching signature in the experimental data, in contrast with some other geometrical constructions like the Fermi surface. However, the particular shape of the Fermi surface of nickel allowed the visualization of the system of edges (skeleton) of the Wigner–Seitz cell of the face-centred cubic lattice in reciprocal space in three dimensions by the diffuse scattering of X-rays from Ni1−xWx(x= 0.03, 0.05, 0.08) single crystals. Employing a cluster-expansion method with first-principles input, it is possible to show that the observed scattering is inherent to the given nickel alloys and the crystal structures they form. This peculiar feature can be understood by considering the shape of the Fermi surface of pure nickel.

Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline

Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and two-photon-excited ultraviolet fluorescence microscopy were evaluated for crystal detection and assessed by X-ray raster scanning. Two optical designs were constructed and characterized; one positioned downstream of the sample and one integrated into the upstream optical path of the diffractometer. Both instruments enabled protein crystal identification with integration times between 80 and 150 µs per pixel, representing a ∼10(3)-10(4)-fold reduction in the per-pixel exposure time relative to X-ray raster scanning. Quantitative centering and analysis of phenylalanine hydroxylase from Chromobacterium violaceum cPAH, Trichinella spiralis deubiquitinating enzyme TsUCH37, human κ-opioid receptor complex kOR-T4L produced in lipidic cubic phase (LCP), intimin prepared in LCP, and α-cellulose samples were performed by collecting multiple NLO images. The crystalline samples were characterized by single-crystal diffraction patterns, while α-cellulose was characterized by fiber diffraction. Good agreement was observed between the sample positions identified by NLO and XRD raster measurements for all samples studied.

High speed X-ray analysis of plant enzymes at room temperature

X-ray measurements at room temperature (295 K) deliver high quality data sets with unprecedented speed (<2 min), as shown for crystallized raucaffricine-O-β-D-glucosidase (RG), its mutant RG-Glu186Gln and several ligand complexes of the enzyme which participates in alkaloid biosynthesis in the plant Rauvolfia. The data obtained are compared with data sets measured under typical cryo conditions (100K). Under both conditions, density maps are highly comparable and favor the described protocol for room temperature measurements, potentially paving the way for future crystallographic studies capturing biosynthetic pathway intermediates.

Upsampling speckle patterns for coherent X-ray diffraction imaging

Coherent X-ray diffraction imaging is a lensless imaging technique where an iterative phase-retrieval algorithm is applied to the speckle pattern, the far-field diffraction pattern produced by an isolated object. To ensure convergence to a unique solution, the diffraction pattern must be oversampled by a factor of two or more. Since the resolution in real space depends on the maximum wave vector where the intensity is detected,i.e.on the detector field of view, there is a practical limitation on oversampling in reciprocal space and resolution in real space that is ultimately determined by the number of pixels. This work shows that it is possible to reduce the effective pixel size and maintain the detector field of view by applying a linear combination method to shifted diffraction patterns. The feasibility of the method is demonstrated by reconstructing the images of test objects from diffraction patterns oversampled in each dimension by factors of 1.3 and 1.8 only. The described approach can be applied to any diffraction or imaging technique where the resolution is compromised by a large pixel size.

An unusual arrangement of two 14-3-3-like domains in the SMG5-SMG7 heterodimer is required for efficient nonsense-mediated mRNA decay

The nonsense-mediated mRNA decay (NMD) pathway triggers the rapid degradation of aberrant mRNAs containing premature translation termination codons (PTCs). In metazoans, NMD requires three 14-3-3-like proteins: SMG5, SMG6, and SMG7. These proteins are recruited to PTC-containing mRNAs through the interaction of their 14-3-3-like domains with phosphorylated UPF1, the central NMD effector. Recruitment of SMG5, SMG6, and SMG7 causes NMD target degradation. In this study, we report the crystal structure of the Caenorhabditis elegans SMG5-SMG7 complex. The 14-3-3-like phosphopeptide recognition domains of SMG5 and SMG7 heterodimerize in an unusual perpendicular back-to-back orientation in which the peptide-binding sites face opposite directions. Structure-based mutants and functional assays indicate that the SMG5-SMG7 interaction is conserved and is crucial for efficient NMD in human cells. Notably, we demonstrate that heterodimerization increases the affinity of the SMG5-SMG7 complex for UPF1. Furthermore, we show that the degradative activity of the SMG5-SMG7 complex resides in SMG7 and that the SMG5-SMG7 complex and SMG6 play partially redundant roles in the degradation of aberrant mRNAs. We propose that the SMG5-SMG7 complex binds to phosphorylated UPF1 with high affinity and recruits decay factors to the mRNA target through SMG7, thus promoting target degradation.

Success and failure of dead-time models as applied to hybrid pixel detectors in high-flux applications

The performance of a single-photon-counting hybrid pixel detector has been investigated at the Australian Synchrotron. Results are compared with the body of accepted analytical models previously validated with other detectors. Detector functionals are valuable for empirical calibration. It is shown that the matching of the detector dead-time with the temporal synchrotron source structure leads to substantial improvements in count rate and linearity of response. Standard implementations are linear up to ∼0.36 MHz pixel(-1); the optimized linearity in this configuration has an extended range up to ∼0.71 MHz pixel(-1); these are further correctable with a transfer function to ∼1.77 MHz pixel(-1). This new approach has wide application both in high-accuracy fundamental experiments and in standard crystallographic X-ray fluorescence and other X-ray measurements. The explicit use of data variance (rather than N(1/2) noise) and direct measures of goodness-of-fit (χ(r)(2)) are introduced, raising issues not encountered in previous literature for any detector, and suggesting that these inadequacies of models may apply to most detector types. Specifically, parametrization of models with non-physical values can lead to remarkable agreement for a range of count-rate, pulse-frequency and temporal structure. However, especially when the dead-time is near resonant with the temporal structure, limitations of these classical models become apparent. Further, a lack of agreement at extreme count rates was evident.

Development of powder diffraction apparatus for small-angle X-ray scattering measurements

A novel type of X-ray collimation system attached to commercial powder diffractometers makes the structural characterization of nanomaterials possible in a wide size range from <0.1 to 100 nm by combination of the small- and wide-angle X-ray scattering techniques. There is no dead interval in the detection between the small- and wide-angle regimes. This device can be attached to any existing `θ/θ' powder diffractometer, providing a multi-functional small- and wide-angle X-ray scattering/diffraction (SWAXS) apparatus. After proper alignment and adjustment, the device can be removed and re-attached at any time to switch between normal and SWAXS functions.

Radiation damage to biological macromolecules: some answers and more questions

Research into radiation damage in macromolecular crystallography has matured over the last few years, resulting in a better understanding of both the processes and timescales involved. In turn this is now allowing practical recommendations for the optimization of crystal dose lifetime to be suggested. Some long-standing questions have been answered by recent investigations, and from these answers new challenges arise and areas of investigation can be proposed. Six papers published in this volume give an indication of some of the current directions of this field and also that of single-particle cryo-microscopy, and the brief summary below places them into the overall framework of ongoing research into macromolecular crystallography radiation damage.