ALBERT

Description: A rare example is reported in which discrete Ag2L2 ring and (AgL)∞ chain motifs [L = N,N′-bis(3-imidazol-1-yl-propyl)-pyromellitic diimide] co-crystallize in the same crystal lattice with varying ratios and degrees of disorder. Crystal structures obtained from representative crystals reveal compatible packing arrangements of the cyclic and polymeric isomers within the crystal lattice, which enables them to co-exist within a crystalline solid solution. A feasible pathway for transformation between the isomers is suggested via facile rotation of the coordinating imidazolyl groups. This chemical system could provide a chance for direct observation of ring-opening isomerization at the crystal surface. Mass spectrometry and 1H NMR titration show a dynamic equilibrium between cyclic and oligomeric species in solution, and a potential crystallization process is suggested involving alignment of precursors directed by aromatic stacking interactions between pyromellitic diimide units, followed by ring-opening isomerization at the interface between the solid and the solution. Both cyclic and oligomeric species can act as precursors, with interconversion between them being facile due to a low energy barrier for rotation of the imidazole rings. Thermogravimetric analysis and variable-temperature powder X-ray diffraction indicate a transition to a different crystalline phase around 120°C, which is associated with loss of solvent from the crystal lattice.

Description: The name of one of the authors in the article by Heymann et al. [(2014), IUCrJ, 1, 349–360] is corrected.

Description: 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.

Description: Crystal structures are presented for two dihydrate polymorphs (DH-I and DH-II) of the non-steroidal anti-inflammatory drug sodium (S)-naproxen. The structure of DH-I is determined from twinned single crystals obtained by solution crystallization. DH-II is obtained by solid-state routes, and its structure is derived using powder X-ray diffraction, solid-state 13C and 23Na MAS NMR, and molecular modelling. The validity of both structures is supported by dispersion-corrected density functional theory (DFT-D) calculations. The structures of DH-I and DH-II, and in particular their relationships to the monohydrate (MH) and anhydrate (AH) structures, provide a basis to rationalize the observed transformation pathways in the sodium (S)-naproxen anhydrate–hydrate system. All structures contain Na+/carboxylate/H2O sections, alternating with sections containing the naproxen molecules. The structure of DH-I is essentially identical to MH in the naproxen region, containing face-to-face arrangements of the naphthalene rings, whereas the structure of DH-II is comparable to AH in the naproxen region, containing edge-to-face arrangements of the naphthalene rings. This structural similarity permits topotactic transformation between AH and DH-II, and between MH and DH-I, but requires re-organization of the naproxen molecules for transformation between any other pair of structures. The topotactic pathways dominate at room temperature or below, while the non-topotactic pathways become active at higher temperatures. Thermochemical data for the dehydration processes are rationalized in the light of this new structural information.

Description: The aim of this article is a general description of the so-called Patterson-function direct methods (PFDM), from their origin to their present state. It covers a 20-year period of methodological contributions to crystal structure solution, most of them published in Acta Crystallographica Section A. The common feature of these variants of direct methods is the introduction of the experimental intensities in the form of the Fourier coefficients of origin-free Patterson-type functions, which allows the active use of both strong and weak reflections. The different optimization algorithms are discussed and their performances compared. This review focuses not only on those PFDM applications related to powder diffraction data but also on some recent results obtained with electron diffraction tomography data.

Description: An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.

Description: The development of semiconductor electronics is reviewed briefly, beginning with the development of germanium devices (band gap Eg = 0.66 eV) after World War II. A tendency towards alternative materials with wider band gaps quickly became apparent, starting with silicon (Eg = 1.12 eV). This improved the signal-to-noise ratio for classical electronic applications. Both semiconductors have a tetrahedral coordination, and by isoelectronic alternative replacement of Ge or Si with carbon or various anions and cations, other semiconductors with wider Eg were obtained. These are transparent to visible light and belong to the group of wide band gap semiconductors. Nowadays, some nitrides, especially GaN and AlN, are the most important materials for optical emission in the ultraviolet and blue regions. Oxide crystals, such as ZnO and β-Ga2O3, offer similarly good electronic properties but still suffer from significant difficulties in obtaining stable and technologically adequate p-type conductivity.

Description: Rv1625c is one of 16 adenylyl cyclases encoded in the genome of Mycobacterium tuberculosis. In solution Rv1625c exists predominantly as a monomer, with a small amount of dimer. It has been shown previously that the monomer is active and the dimeric fraction is inactive. Both fractions of wild-type Rv1625c crystallized as head-to-head inactive domain-swapped dimers as opposed to the head-to-tail dimer seen in other functional adenylyl cyclases. About half of the molecule is involved in extensive domain swapping. The strain created by a serine residue located on a hinge loop and the crystallization condition might have led to this unusual domain swapping. The inactivity of the dimeric form of Rv1625c could be explained by the absence of the required catalytic site in the swapped dimer. A single mutant of the enzyme was also generated by changing a phenylalanine predicted to occur at the functional dimer interface to an arginine. This single mutant exists as a dimer in solution but crystallized as a monomer. Analysis of the structure showed that a salt bridge formed between a glutamate residue in the N-terminal segment and the mutated arginine residue hinders dimer formation by pulling the N-terminal region towards the dimer interface. Both structures reported here show a change in the dimerization-arm region which is involved in formation of the functional dimer. It is concluded that the dimerization arm along with other structural elements such as the N-terminal region and certain loops are vital for determining the oligomeric nature of the enzyme, which in turn dictates its activity.

Description: Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

Description: CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.

Description: The structure and mechanical properties of crystalline materials of three boron difluoride dibenzoylmethane (BF2dbm) derivatives were investigated to examine the correlation, if any, among mechanochromic luminescence (ML) behaviour, solid-state structure, and the mechanical behaviour of single crystals. Qualitative mechanical deformation tests show that the crystals of BF2dbm(tBu)2 can be bent permanently, whereas those of BF2dbm(OMe)2 exhibit an inhomogeneous shearing mode of deformation, and finally BF2dbmOMe crystals are brittle. Quantitative mechanical analysis by nanoindentation on the major facets of the crystals shows that BF2dbm(tBu)2 is soft and compliant with low values of elastic modulus, E, and hardness, H, confirming its superior suceptibility for plastic deformation, which is attributed to the presence of a multitude of slip systems in the crystal structure. In contrast, both BF2dbm(OMe)2 and BF2dbmOMe are considerably stiffer and harder with comparable E and H, which are rationalized through analysis of the structural attributes such as the intermolecular interactions, slip systems and their relative orientation with respect to the indentation direction. As expected from the qualitative mechanical behaviour, prominent ML was observed in BF2dbm(tBu)2, whereas BF2dbm(OMe)2 exhibits only a moderate ML and BF2dbmOMe shows no detectable ML, all examined under identical conditions. These results confirm that the extent of ML in crystalline organic solid-state fluorophore materials can be correlated positively with the extent of plasticity (low recovery). In turn, they offer opportunities to design new and improved efficient ML materials using crystal engineering principles.

Description: In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1) an overview and historical review of halogen bonding; (2) exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3) the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4) strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

Description: Characterization of transverse coherence is one of the most critical themes for advanced X-ray sources and their applications in many fields of science. However, for hard X-ray free-electron laser (XFEL) sources there is very little knowledge available on their transverse coherence characteristics, despite their extreme importance. This is because the unique characteristics of the sources, such as the ultra-intense nature of XFEL radiation and the shot-by-shot fluctuations in the intensity distribution, make it difficult to apply conventional techniques. Here, an extended Young's interference experiment using a stream of bimodal gold particles is shown to achieve a direct measurement of the modulus of the complex degree of coherence of XFEL pulses. The use of interference patterns from two differently sized particles enables analysis of the transverse coherence on a single-shot basis without a priori knowledge of the instantaneous intensity ratio at the particles. For a focused X-ray spot as small as 1.8 µm (horizontal) × 1.3 µm (vertical) with an ultrahigh intensity that exceeds 1018 W cm−2 from the SPring-8 Ångstrom Compact free-electron LAser (SACLA), the coherence lengths were estimated to be 1.7 ± 0.2 µm (horizontal) and 1.3 ± 0.1 µm (vertical). The ratios between the coherence lengths and the focused beam sizes are almost the same in the horizontal and vertical directions, indicating that the transverse coherence properties of unfocused XFEL pulses are isotropic. The experiment presented here enables measurements free from radiation damage and will be readily applicable to the analysis of the transverse coherence of ultra-intense nanometre-sized focused XFEL beams.

Description: Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

Description: The synchrotron through-the-substrate X-ray microdiffraction technique (tts-μXRD) is extended to the structural study of microvolumes of crystals embedded in polished thin sections of compact materials [Rius, Labrador, Crespi, Frontera, Vallcorba & Melgarejo (2011). J.Synchrotron Rad. 18, 891–898]. The resulting tts-μXRD procedure includes some basic steps: (i) collection of a limited number of consecutive two-dimensional patterns (frames) for each randomly oriented crystal microvolume; (ii) refinement of the metric from the one-dimensional diffraction pattern which results from circularly averaging the sum of collected frames; (iii) determination of the reciprocal lattice orientation of each randomly oriented crystal microvolume which allows assigning the hkl indices to the spots and, consequently, merging the intensities of the different frames into a single-crystal data set (frame merging); and (iv) merging of the individual crystal data sets (multicrystal merging) to produce an extended data set suitable for structure refinement/solution. Its viability for crystal structure solution by Patterson function direct methods (δ recycling) and for accurate single-crystal least-squares refinements is demonstrated with some representative examples from petrology in which different glass substrate thicknesses have been employed. The section of the crystal microvolume must be at least of the same order of magnitude as the focus of the beam (15 × 15 µm in the provided examples). Thanks to its versatility and experimental simplicity, this methodology should be useful for disciplines as disparate as petrology, materials science and cultural heritage.

Description: The crystallization of 28 binary and ternary cocrystals of quercetin with dibasic coformers is analyzed in terms of a combinatorial selection from a solution of preferred molecular conformations and supramolecular synthons. The crystal structures are characterized by distinctive O—H...N and O—H...O based synthons and are classified as nonporous, porous and helical. Variability in molecular conformation and synthon structure led to an increase in the energetic and structural space around the crystallization event. This space is the crystal structure landscape of the compound and is explored by fine-tuning the experimental conditions of crystallization. In the landscape context, we develop a strategy for the isolation of ternary cocrystals with the use of auxiliary template molecules to reduce the molecular and supramolecular `confusion' that is inherent in a molecule like quercetin. The absence of concomitant polymorphism in this study highlights the selectivity in conformation and synthon choice from the virtual combinatorial library in solution.

Description: Published diffuse X-ray scattering from the high-Tc superconductor HgBa2CuO4+δ has been reexamined with a view to developing a model that more satisfactorily accounts for the observed patterns. The present work agrees with the previous conclusion that the doping oxygen atoms form long and isolated interstitial chains that run in both tetragonal directions. However, a distinctly different model is proposed for the accompanying displacement patterns of the atoms surrounding these linear defects. In this new model it is proposed that it is the correlated shifts of the Ba atoms along the length of the defect chains that are the primary source of the observed scattering, and that the variations of intensity in the generated diffuse streaks of scattering originate from lateral shifts of both Hg and Ba atoms away from defects. The new model yields diffraction patterns that are in much more convincing agreement with the observations than the original model.

Description: Carbonic anhydrases (CAs; EC 4.2.1.1) catalyze the interconversion of CO2 and HCO3−, and their inhibitors have long been used as diuretics and as a therapeutic treatment for many disorders such as glaucoma and epilepsy. Acetazolamide (AZM) and methazolamide (MZM, a methyl derivative of AZM) are two of the classical CA inhibitory drugs that have been used clinically for decades. The jointly refined X-ray/neutron structure of MZM in complex with human CA isoform II (hCA II) has been determined to a resolution of 2.2 Å with an Rcryst of ∼16.0%. Presented in this article, along with only the second neutron structure of a clinical drug-bound hCA, is an in-depth structural comparison and analyses of differences in hydrogen-bonding network, water-molecule orientation and solvent displacement that take place upon the binding of AZM and MZM in the active site of hCA II. Even though MZM is slightly more hydrophobic and displaces more waters than AZM, the overall binding affinity (Ki) for both of the drugs against hCA II is similar (∼10 nM). The plausible reasons behind this finding have also been discussed using molecular dynamics and X-ray crystal structures of hCA II–MZM determined at cryotemperature and room temperature. This study not only allows a direct comparison of the hydrogen bonding, protonation states and solvent orientation/displacement of AZM and MZM, but also shows the significant effect that the methyl derivative has on the solvent organization in the hCA II active site.

Description: A tyrosyl radical, as part of the amino acid chain of bovine liver catalase, supports dynamic proton spin polarization (DNP). Finding the position of the tyrosyl radical within the macromolecule relies on the accumulation of proton polarization close to it, which is readily observed by polarized neutron scattering. The nuclear scattering amplitude due to the polarization of protons less than 10 Å distant from the tyrosyl radical is ten times larger than the amplitude of magnetic neutron scattering from an unpaired polarized electron of the same radical. The direction of DNP was inverted every 5 s, and the initial evolution of the intensity of polarized neutron scattering after each inversion was used to identify those tyrosines which have assumed a radical state. Three radical sites, all of them close to the molecular centre and the haem, appear to be equally possible. Among these is tyr-369, the radical state of which had previously been proven by electron paramagnetic resonance.

Description: The design of novel supramolecular synthons for functional groups relevant to drugs is an essential prerequisite for applying crystal engineering in the development of novel pharmaceutical cocrystals. It has been convincingly shown over the past decade that molecular level control and modulation can influence the physicochemical properties of drug cocrystals. Whereas considerable advances have been reported on the design of cocrystals for carboxylic acids and carboxamide functional groups, the sulfonamide group, which is a cornerstone of sulfa drugs, is relatively unexplored for reproducible heterosynthon-directed crystal engineering. The occurrence of synthons and isostructurality in sulfonamide–lactam cocrystals (SO2NH2...CONH hydrogen bonding) is analyzed to define a strategy for amide-type GRAS (generally recognized as safe) coformers with sulfonamides. Three types of supramolecular synthons are identified for the N—H donor of sulfonamide hydrogen bonding to the C=O acceptor of amide. Synthon 1: catemer synthon C21(4) chain motif, synthon 2: dimer–cyclic ring synthon R22(8)R42(8) motifs, and synthon 3: dimer–catemer synthon of R22(8)C11(4)D notation. These heterosynthons of the cocrystals observed in this study are compared with the N—H...O dimer R22(8) ring and C(4) chain motifs of the individual sulfonamide structures. The X-ray crystal structures of sulfonamide–lactam cocrystals exhibit interesting isostructurality trends with the same synthon being present. One-dimensional, two-dimensional and three-dimensional isostructurality in crystal structures is associated with isosynthons and due to their recurrence, novel heterosynthons for sulfonamide cocrystals are added to the crystal engineer's toolkit. With the predominance of sulfa drugs in medicine, these new synthons provide rational strategies for the design of binary and potentially ternary cocrystals of sulfonamides.

Description: The authors' experience of the application of X-ray diffraction imaging in carrying out space technological experiments on semiconductor crystal growth for the former USSR and for Russia is reported, from the Apollo–Soyuz programme (1975) up to the present day. X-ray topography was applied to examine defects in crystals in order to obtain information on the crystallization conditions and also on their changes under the influence of factors of orbital flight in space vehicles. The data obtained have promoted a deeper understanding of the conditions and mechanisms of crystallization under both microgravity and terrestrial conditions, and have enabled the elaboration of terrestrial methods of highly perfect crystal growth. The use of X-ray topography in space materials science has enriched its methods in the field of digital image processing of growth striations and expanded its possibilities in investigating the inhomogeneity of crystals.

Description: Using synchrotron X-ray powder diffraction, the structure of a co-crystal between benzene and ethane formed in situ at cryogenic conditions has been determined, and validated using dispersion-corrected density functional theory calculations. The structure comprises a lattice of benzene molecules hosting ethane molecules within channels. Similarity between the intermolecular interactions found in the co-crystal and in pure benzene indicate that the C—H...π network of benzene is maintained in the co-crystal, however, this expands to accommodate the guest ethane molecules. The co-crystal has a 3:1 benzene:ethane stoichiometry and is described in the space group R\bar 3 with a = 15.977 (1) Å and c = 5.581 (1) Å at 90 K, with a density of 1.067 g cm−3. The conditions under which this co-crystal forms identify it is a potential that forms from evaporation of Saturn's moon Titan's lakes, an evaporite material.

Description: Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.

Description: This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50–8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.

Description: A new monoclinic polymorph, form II (P21/c, Z = 4), has been isolated for 3,4-dimethoxycinnamic acid (DMCA). Its solid-state 2 + 2 photoreaction to the corresponding α-truxillic acid is different from that of the first polymorph, the triclinic form I (P\bar 1, Z = 4) that was reported in 1984. The crystal structures of the two forms are rather different. The two polymorphs also exhibit different photomechanical properties. Form I exhibits photosalient behavior but this effect is absent in form II. These properties can be explained on the basis of the crystal packing in the two forms. The nanoindentation technique is used to shed further insights into these structure−property relationships. A faster photoreaction in form I and a higher yield in form II are rationalized on the basis of the mechanical properties of the individual crystal forms. It is suggested that both Schmidt-type and Kaupp-type topochemistry are applicable for the solid-state trans-cinnamic acid photodimerization reaction. Form I of DMCA is more plastic and seems to react under Kaupp-type conditions with maximum molecular movements. Form II is more brittle, and its interlocked structure seems to favor Schmidt-type topochemistry with minimum molecular movement.

Description: By means of normal-incidence, high-flux and high-energy X-rays, total scattering data for pair distribution function (PDF) analysis have been obtained from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. The `tfPDF' method is illustrated through studies of as-deposited (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows the prediction of whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films.

Description: Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

Description: A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can be extended to multiphase nanocrystalline materials as well. Thus, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.

Description: We report a molecular crystal that exhibits four successive phase transitions under hydrostatic pressure, driven by aurophilic interactions, with the ground-state structure re-emerging at high pressure. The effect of pressure on two polytypes of tris(μ2-3,5-diisopropyl-1,2,4-triazolato-κ2N1:N2)trigold(I) (denoted Form-I and Form-II) has been analysed using luminescence spectroscopy, single-crystal X-ray diffraction and first-principles computation. A unique phase behaviour was observed in Form-I, with a complex sequence of phase transitions between 1 and 3.5 GPa. The ambient C2/c mother cell transforms to a P21/n phase above 1 GPa, followed by a P21/a phase above 2 GPa and a large-volume C2/c supercell at 2.70 GPa, with the previously observed P21/n phase then reappearing at higher pressure. The observation of crystallographically identical low- and high-pressure P21/n phases makes this a rare example of a re-entrant phase transformation. The phase behaviour has been characterized using detailed crystallographic theory and modelling, and rationalized in terms of molecular structural distortions. The dramatic changes in conformation are correlated with shifts of the luminescence maxima, from a band maximum at 14040 cm−1 at 2.40 GPa, decreasing steeply to 13550 cm−1 at 3 GPa. A similar study of Form-II displays more conventional crystallographic behaviour, indicating that the complex behaviour observed in Form-I is likely to be a direct consequence of the differences in crystal packing between the two polytypes.

Description: SnTe is a promising thermoelectric and topological insulator material. Here, the presumably simple rock salt crystal structure of SnTe is studied comprehensively by means of high-resolution synchrotron single-crystal and powder X-ray diffraction from 20 to 800 K. Two samples with different carrier concentrations (sample A = high, sample B = low) have remarkably different atomic displacement parameters, especially at low temperatures. Both samples contain significant numbers of cation vacancies (1–2%) and ordering of Sn vacancies possibly occurs on warming, as corroborated by the appearance of multiple phases and strain above 400 K. The possible presence of disorder and anharmonicity is investigated in view of the low thermal conductivity of SnTe. Refinement of anharmonic Gram–Charlier parameters reveals marginal anharmonicity for sample A, whereas sample B exhibits anharmonic effects even at low temperature. For both samples, no indications are found of a low-temperature rhombohedral phase. Maximum entropy method (MEM) calculations are carried out, including nuclear-weighted X-ray MEM calculations (NXMEM). The atomic electron densities are spherical for sample A, whereas for sample B the Te electron density is elongated along the 〈100〉 direction, with the maximum being displaced from the lattice position at higher temperatures. Overall, the crystal structure of SnTe is found to be defective and sample-dependent, and therefore theoretical calculations of perfect rock salt structures are not expected to predict the properties of real materials.

Description: The solid-state phase transitions and intermediate structures of S-2-aminobutanoic acid (l-2-aminobutyric acid), S-2-aminopentanoic acid (l-norvaline), S-2-aminohexanoic acid (l-norleucine) and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.

Description: Temperature and composition dependences of the I41/amd → Fd\bar 3m phase transition in the MgxCu1 − xCr2O4 spinel solid solution, due to the melting of the cooperative Jahn–Teller distortion, have been studied by means of single-crystal X-ray diffraction. Crystals with x = 0, 0.10, 0.18, 0.43, 0.46, 0.53, 1 were grown by flux decomposition methods. All crystals have been refined in the tetragonal I41/amd space group except for the Mg end-member, which has cubic symmetry. In MgxCu1 − xCr2O4 the progressive substitution of the Jahn–Teller, d9 Cu2+ cation with spherical and closed-shell Mg2+ has a substantial effect on the crystal structure, such that there is a gradual reduction of the splitting of a and c unit-cell parameters and flattening of the tetrahedra. Single-crystal diffraction data collected in situ up to T = 1173 K show that the tetragonal-to-cubic transition temperature decreases with increasing Mg content. The strength of the Cu—Cu interaction is, in effect, modulated by varying the Cu/Mg ratio. Structure refinements of diffraction data collected at different temperatures reveal that heating results in a gradual reduction in the tetrahedron compression, which remains significant until near the transition temperature, however, at which point the distortion of the tetrahedra rapidly vanishes. The spontaneous strain arising in the tetragonal phase is large, amounting to 10% shear strain, et, and ∼ 1% volume strain, Vs, in the copper chromite end-member at room temperature. Observed strain relationships are consistent with pseudoproper ferroelastic behaviour (e_{\rm t}^2 ∝ Vs ∝ q_{\rm JT}^2, where qJT is the order parameter). The I41/amd → Fd\bar 3m phase transition is first order in character for Cu-rich samples and then evolves towards second-order character. Although a third order term is permitted by symmetry in the Landau expansion, this behaviour appears to be more accurately represented by a 246 expansion with a change from negative to positive values of the fourth-order coefficient with progressive dilution of the Jahn–Teller cation.

Description: Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein–Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.

Description: During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the `self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5–10 fs, but can succeed for pulses 50–100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage (`damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30–50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

Description: Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.

Description: The isolation and characterization of small sulfur allotropes have long remained unachievable because of their extreme lability. This study reports the first direct observation of disulfur (S2) with X-ray crystallography. Sulfur gas was kinetically trapped and frozen into the pores of two Cu-based porous coordination networks containing interactive iodide sites. Stabilization of S2 was achieved either through physisorption or chemisorption on iodide anions. One of the networks displayed shape selectivity for linear molecules only, therefore S2 was trapped and remained stable within the material at room temperature and higher. In the second network, however, the S2 molecules reacted further to produce bent-S3 species as the temperature was increased. Following the thermal evolution of the S2 species in this network using X-ray diffraction and Raman spectroscopy unveiled the generation of a new reaction intermediate never observed before, the cyclo-trisulfur dication (cyclo-S32+). It is envisaged that kinetic guest trapping in interactive crystalline porous networks will be a promising method to investigate transient chemical species.

Description: The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.

Description: Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07–1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a `catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

Description: For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (`decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

Description: Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.

Description: Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow `highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a `first-choice' method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development.

Description: The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen...halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C...C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C—H...Cl and O—H...O are the preferred interactions in compounds containing both O and Cl.

Description: Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular interactions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co-crystals or eutectics for the studied carboxylic acid/imide combinations.

Description: New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of data can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.

Description: Small-angle X-ray and neutron scattering (SAXS and SANS) experiments on solutions provide rapidly decaying scattering curves, often with a poor signal-to-noise ratio, especially at higher angles. On modern instruments, the noise is partially compensated for by oversampling, thanks to the fact that the angular increment in the data is small compared with that needed to describe adequately the local behaviour and features of the scattering curve. Given a (noisy) experimental data set, an important question arises as to which part of the data still contains useful information and should be taken into account for the interpretation and model building. Here, it is demonstrated that, for monodisperse systems, the useful experimental data range is defined by the number of meaningful Shannon channels that can be determined from the data set. An algorithm to determine this number and thus the data range is developed, and it is tested on a number of simulated data sets with various noise levels and with different degrees of oversampling, corresponding to typical SAXS/SANS experiments. The method is implemented in a computer program and examples of its application to analyse the experimental data recorded under various conditions are presented. The program can be employed to discard experimental data containing no useful information in automated pipelines, in modelling procedures, and for data deposition or publication. The software is freely accessible to academic users.

Description: Current trends for X-ray imaging detectors based on hybrid and monolithic detector technologies are reviewed. Hybrid detectors with photon-counting pixels have proven to be very powerful tools at synchrotrons. Recent developments continue to improve their performance, especially for higher spatial resolution at higher count rates with higher frame rates. Recent developments for X-ray free-electron laser (XFEL) experiments provide high-frame-rate integrating detectors with both high sensitivity and high peak signal. Similar performance improvements are sought in monolithic detectors. The monolithic approach also offers a lower noise floor, which is required for the detection of soft X-ray photons. The link between technology development and detector performance is described briefly in the context of potential future capabilities for X-ray imaging detectors.

Description: X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. The EMC algorithm [Loh & Elser (2009), Phys. Rev. E, 80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philipp et al. (2012), Opt. Express, 20, 13129–13137; Ayyer et al. (2014), Opt. Express, 22, 2403–2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35 kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.

Description: Structural and functional studies require the development of sophisticated `Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB `super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Description: To satisfy the needs of rapidly growing applications, Li-ion batteries require further significant improvements of their key properties: specific energy and power, cyclability, safety and costs. The first generation of cathode materials for Li-ion batteries based on mixed oxides with either spinel or rock-salt derivatives has already been widely commercialized, but the potential to improve the performance of these materials further is almost exhausted. Li and transition metal inorganic compounds containing different polyanions are now considered as the most promising cathode materials for the next generation of Li-ion batteries. Further advances in cathode materials are considered to lie in combining different anions [such as (XO4)n− and F−] in the anion sublattice, which is expected to enhance the specific energy and power of these materials. This review focuses on recent advances related to the new class of cathode materials for Li-ion batteries containing phosphate and fluoride anions. Special attention is given to their crystal structures and the relationships between structure and properties, which are important for their possible practical applications.

Description: Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a `still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

Description: In the 20 years since precession electron diffraction (PED) was introduced, it has grown from a little-known niche technique to one that is seen as a cornerstone of electron crystallography. It is now used primarily in two ways. The first is to determine crystal structures, to identify lattice parameters and symmetry, and ultimately to solve the atomic structure ab initio. The second is, through connection with the microscope scanning system, to map the local orientation of the specimen to investigate crystal texture, rotation and strain at the nanometre scale. This topical review brings the reader up to date, highlighting recent successes using PED and providing some pointers to the future in terms of method development and how the technique can meet some of the needs of the X-ray crystallography community. Complementary electron techniques are also discussed, together with how a synergy of methods may provide the best approach to electron-based structure analysis.

Description: IgG subclass-specific differences in biological function and in vitro stability are often referred to variations in the conformational flexibility, while this flexibility has rarely been characterized. Here, small-angle X-ray scattering data from IgG1, IgG2 and IgG4 antibodies, which were designed with identical variable regions, were thoroughly analysed by the ensemble optimization method. The extended analysis of the optimized ensembles through shape clustering reveals distinct subclass-specific conformational preferences, which provide new insights for understanding the variations in physical/chemical stability and biological function of therapeutic antibodies. Importantly, the way that specific differences in the linker region correlate with the solution structure of intact antibodies is revealed, thereby visualizing future potential for the rational design of antibodies with designated physicochemical properties and tailored effector functions. In addition, this advanced computational approach is applicable to other flexible multi-domain systems and extends the potential for investigating flexibility in solutions of macromolecules by small-angle X-ray scattering.

Description: The crystal structure of the high-temperature paraelectric phase of Rochelle salt (K+·Na+·C4H4O62−·4H2O) at 308 K has been reinvestigated using synchrotron X-ray diffraction with refinement parameters R(int) = 0.0123, final (shift/e.s.d.)max = 0.019, R1(all) = 0.0371 and wR2(all) = 0.0608. The application of a new gas-flow sample cell designed to control both temperature and relative humidity permitted collection of data of excellent quality and enabled unrestrained refinement of all parameters, including those of the isotropic hydrogen atoms. A precise description of the structure has ensued. One K atom is disordered between two symmetry-equivalent sites; three O atoms in three of the four water molecules exhibit very strong anisotropy. Refining one O atom as a split atom was successful, yielding small improvements in the bonding parameters of several H atoms. The H atoms of all water molecules behave as single pairs. Their final U values are of moderate magnitude indicating that these atoms do not participate in the anisotropy of the parent O atoms. It is suggested that the three water O atoms are in part statically disordered, while the bonded H atoms are not. Except for the split K atom and the three water O atoms there is no evidence of general disorder in the structure.

Description: The usefulness of a modulation wave approach to understanding and interpreting the highly structured continuous diffuse intensity distributions characteristic of the reciprocal spaces of the very large family of inherently flexible materials which exhibit ordered `disorder' is pointed out. It is shown that both longer range order and truly short-range order are simultaneously encoded in highly structured diffuse intensity distributions. The long-range ordered crystal chemical rules giving rise to such diffuse distributions are highlighted, along with the existence and usefulness of systematic extinction conditions in these types of structured diffuse distributions.

Description: Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation.

Description: Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

Description: Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.

Description: Structural studies in general, and crystallography in particular, have benefited and still do benefit dramatically from the use of synchrotron radiation. Low-emittance storage rings of the third generation provide focused beams down to the micrometre range that are sufficiently intense for the investigation of weakly scattering crystals down to the size of several micrometres. Even though the coherent fraction of these sources is below 1%, a number of new imaging techniques have been developed to exploit the partially coherent radiation. However, many techniques in nanoscience are limited by this rather small coherent fraction. On the one hand, this restriction limits the ability to study the structure and dynamics of non-crystalline materials by methods that depend on the coherence properties of the beam, like coherent diffractive imaging and X-ray correlation spectroscopy. On the other hand, the flux in an ultra-small diffraction-limited focus is limited as well for the same reason. Meanwhile, new storage rings with more advanced lattice designs are under construction or under consideration, which will have significantly smaller emittances. These sources are targeted towards the diffraction limit in the X-ray regime and will provide roughly one to two orders of magnitude higher spectral brightness and coherence. They will be especially suited to experiments exploiting the coherence properties of the beams and to ultra-small focal spot sizes in the regime of several nanometres. Although the length of individual X-ray pulses at a storage-ring source is of the order of 100 ps, which is sufficiently short to track structural changes of larger groups, faster processes as they occur during vision or photosynthesis, for example, are not accessible in all details under these conditions. Linear accelerator (linac) driven free-electron laser (FEL) sources with extremely short and intense pulses of very high coherence circumvent some of the limitations of present-day storage-ring sources. It has been demonstrated that their individual pulses are short enough to outrun radiation damage for single-pulse exposures. These ultra-short pulses also enable time-resolved studies 1000 times faster than at standard storage-ring sources. Developments are ongoing at various places for a totally new type of X-ray source combining a linac with a storage ring. These energy-recovery linacs promise to provide pulses almost as short as a FEL, with brilliances and multi-user capabilities comparable with a diffraction-limited storage ring. Altogether, these new X-ray source developments will provide smaller and more intense X-ray beams with a considerably higher coherent fraction, enabling a broad spectrum of new techniques for studying the structure of crystalline and non-crystalline states of matter at atomic length scales. In addition, the short X-ray pulses of FELs will enable the study of fast atomic dynamics and non-equilibrium states of matter.

Description: In situ and in operando studies are commonplace and necessary in functional materials research. This review highlights recent developments in the analysis of functional materials using state-of-the-art in situ and in operando X-ray and neutron scattering and analysis. Examples are given covering a number of important materials areas, alongside a description of the types of information that can be obtained and the experimental setups used to acquire them.

Description: A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.

Description: Multiple light-induced reversible metastable NO linkage isomers (PLIs) have been detected in the dinitrosyl compound [RuCl(NO)2(PPh3)2]BF4 by a combination of photocrystallographic and IR analysis. The IR signature of three PLI states has been clearly identified, with estimated populations of 59% (PLI-1), 8% (PLI-2) and 5% (PLI-3) for a total population of the metastable state of 72%. The structural configuration of the major component (PLI-1) has been derived by X-ray photocrystallography. In the ground state, the structure is characterized by a bent and a linear nitrosyl, the bent one being oriented towards the linear equatorial nitrosyl with an Ru—N—O angle of 133.88 (9)°. X-ray Fourier difference maps indicate a selectivity of the photo-isomerization process in PLI-1: only the bent NO ligand changes its position, while the linear NO is unaffected. After irradiation at 405 nm, the orientation is changed by rotation towards the Cl ligand opposite the linear NO, with an Ru—N—O angle in this new position of 109 (1)°. The photocrystallographic analysis provides evidence that, in the photo-induced metastable state, the bent NO group is attached to the Ru atom through the N atom (Ru—N—O), rather than in an isonitrosyl Ru—O—N binding mode. In the IR spectra, the asymmetric NO vibrational band shifts by −33 cm−1 to a lower value, whereas the symmetric band splits and shifts by 5 cm−1 to a higher value and by −8 cm−1 to a lower value. The down shift is a clear indication of the structural change, and the small upward shift in response to the new electronic configuration of the metastable structure. Variable-temperature IR kinetic measurements in the range 80–114 K show that the decay of the PLI-1 state follows an Arrhenius behaviour with an activation energy of 0.22 eV.

Description: This article reports unique pattern formation processes and mechanisms via crystallization of materials under external flow fields as one of the general problems of open nonequilibrium phenomena in statistical physics. The external fields effectively reduce step-by-step the exceedingly large free energy barriers associated with the reduction of the enormously large entropy necessary for crystallization into unique crystalline textures in the absence of the fields. The cascading reduction of the free energy barrier was discovered to be achieved as a consequence of a cascading evolution of a series of dissipative structures. Moreover, this cascading pattern evolution obeys the Ginzburg–Landau law. It first evolves a series of large-length-scale amorphous precursors driven by liquid–liquid phase separation under a relatively low bulk stress and then small-length-scale structures driven by a large local stress concentrated on the heterogeneous amorphous precursors, eventually leading to the formation of unique crystalline textures which cannot be developed free from the external fields. Here the multi-length-scale heterogeneous structures developed in the amorphous precursors play a dominant role in the triggering of the crystallization in the local regions subjected to a large stress concentration even under a relatively small applied bulk stress.

Description: The complex nano-morphology of modern soft-matter materials is successfully probed with advanced grazing-incidence techniques. Based on grazing-incidence small- and wide-angle X-ray and neutron scattering (GISAXS, GIWAXS, GISANS and GIWANS), new possibilities arise which are discussed with selected examples. Due to instrumental progress, highly interesting possibilities for local structure analysis in this material class arise from the use of micro- and nanometer-sized X-ray beams in micro- or nanofocused GISAXS and GIWAXS experiments. The feasibility of very short data acquisition times down to milliseconds creates exciting possibilities for in situ and in operando GISAXS and GIWAXS studies. Tuning the energy of GISAXS and GIWAXS in the soft X-ray regime and in time-of flight GISANS allows the tailoring of contrast conditions and thereby the probing of more complex morphologies. In addition, recent progress in software packages, useful for data analysis for advanced grazing-incidence techniques, is discussed.

Description: An overview is given of the recent advances in the field of modulated molecular and inorganic crystals with an emphasis on the links between incommensurability, intermolecular and interatomic interactions and, wherever possible, the properties of the materials. The importance of detailed knowledge on the modulated structure for understanding the crystal chemistry and the functional properties of modulated phases is shown using selected examples of incommensurate modulations in organic molecular compounds and inorganic complex oxides.

Description: Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.

Description: Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2). For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.

Description: More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal–organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium `High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.

Description: The crystal structures of eight mono-methyl alkanes have been determined from single-crystal or high-resolution powder X-ray diffraction using synchrotron radiation. Mono-methyl alkanes can be found on the cuticles of insects and are believed to act as recognition pheromones in some social species, e.g. ants, wasps etc. The molecules were synthesized as pure S enantiomers and are (S)-9-methylpentacosane, C26H54; (S)-9-methylheptacosane and (S)-11-methylheptacosane, C28H58; (S)-7-methylnonacosane, (S)-9-methylnonacosane, (S)-11-methylnonacosane and (S)-13-methylnonacosane, C30H62; and (S)-9-methylhentriacontane, C32H66. All crystallize in space group P21. Depending on the position of the methyl group on the carbon chain, two packing schemes are observed, in which the molecules pack together hexagonally as linear rods with terminal and side methyl groups clustering to form distinct motifs. Carbon-chain torsion angles deviate by less than 10° from the fully extended conformation, but with one packing form showing greater curvature than the other near the position of the methyl side group. The crystal structures are optimized by dispersion-corrected DFT calculations, because of the difficulties in refining accurate structural parameters from powder diffraction data from relatively poorly crystalline materials.

Description: The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges 〉100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c′, are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Description: Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

Description: X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

Description: Nondestructive measurements of the full elastic strain and stress tensors from individual dislocation cells distributed along the full extent of a 50 µm-long polycrystalline copper via in Si is reported. Determining all of the components of these tensors from sub-micrometre regions within deformed metals presents considerable challenges. The primary issues are ensuring that different diffraction peaks originate from the same sample volume and that accurate determination is made of the peak positions from plastically deformed samples. For these measurements, three widely separated reflections were examined from selected, individual grains along the via. The lattice spacings and peak positions were measured for multiple dislocation cell interiors within each grain and the cell-interior peaks were sorted out using the measured included angles. A comprehensive uncertainty analysis using a Monte Carlo uncertainty algorithm provided uncertainties for the elastic strain tensor and stress tensor components.

Description: Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax 〉 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ   65°.

Description: Through X-ray crystallographic fragment screening, 4-bromopyrazole was discovered to be a `magic bullet' that is capable of binding at many of the ligand `hot spots' found in HIV-1 reverse transcriptase (RT). The binding locations can be in pockets that are `hidden' in the unliganded crystal form, allowing rapid identification of these sites for in silico screening. In addition to hot-spot identification, this ubiquitous yet specific binding provides an avenue for X-ray crystallographic phase determination, which can be a significant bottleneck in the determination of the structures of novel proteins. The anomalous signal from 4-bromopyrazole or 4-iodopyrazole was sufficient to determine the structures of three proteins (HIV-1 RT, influenza A endonuclease and proteinase K) by single-wavelength anomalous dispersion (SAD) from single crystals. Both compounds are inexpensive, readily available, safe and very soluble in DMSO or water, allowing efficient soaking into crystals.

Description: In this overview, we briefly outline recent advances in electron cryomicroscopy (cryoEM) and explain why the journal IUCrJ, published by the International Union of Crystallography, could provide a natural home for publications covering many present and future developments in the cryoEM field.

Description: A novel design strategy for cocrystals of a sulfonamide drug with pyridine carboxamides and cyclic amides is developed based on synthon identification as well as size and shape match of coformers. Binary adducts of acetazolamide (ACZ) with lactams (valerolactam and caprolactam, VLM, CPR), cyclic amides (2-pyridone, labeled as 2HP and its derivatives MeHP, OMeHP) and pyridine amides (nicotinamide and picolinamide, NAM, PAM) were obtained by manual grinding, and their single crystals by solution crystallization. The heterosynthons in the binary cocrystals of ACZ with these coformers suggested a ternary combination for ACZ with pyridone and nicotinamide. Novel supramolecular synthons of ACZ with lactams and pyridine carboxamides are reported together with binary and ternary cocrystals for a sulfonamide drug. This crystal engineering study resulted in the first ternary cocrystal of acetazolamide with amide coformers, ACZ–NAM–2HP (1:1:1).

Description: Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H...H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

Description: X-ray scattering images collected on timescales shorter than rotation diffusion times using a (partially) coherent beam result in a significant increase in information content in the scattered data. These measurements, named fluctuation X-ray scattering (FXS), are typically performed on an X-ray free-electron laser (XFEL) and can provide fundamental insights into the structure of biological molecules, engineered nanoparticles or energy-related mesoscopic materials beyond what can be obtained with standard X-ray scattering techniques. In order to understand, use and validate experimental FXS data, the availability of basic data characteristics and operational properties is essential, but has been absent up to this point. In this communication, an intuitive view of the nature of FXS data and their properties is provided, the effect of FXS data on the derived structural models is highlighted, and generalizations of the Guinier and Porod laws that can ultimately be used to plan experiments and assess the quality of experimental data are presented.

Description: Second harmonic generation (SHG) is a well known non-linear optical phenomena which can be observed only in non-centrosymmetric crystals due to non-zero hyperpolarizability. In the current work we observed SHG from a Zn(II) complex which was originally thought to have crystallized in the centrosymmetric space group C2/c. This has been attributed to the unequal antiparallel packing of the metal complexes in the non-symmetric space group Cc or residual non-centrosymmetry in C2/c giving rise to polarizability leading to strong SHG. The enhancement of SHG by UV light has been attributed to the increase in non-centrosymmetry and hence polarity of packing due to strain induced in the crystals. The SHG signals measured from these crystals were as large as potassium dihydrogen phosphate crystals, KH2PO4 (KDP), and showed temperature dependence. The highest SHG efficiency was observed at 50 K. The SHG phenomenon was observed at broad wavelengths ranging from visible to below-red in these crystals.