ALBERT

Beschreibung: A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data (PDFitc) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping, are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc. In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.

Beschreibung: Experimental values of atomic positions in the β-Mn crystal permit one to distinguish among them a fragment of the helix containing 15 interpenetrating distorted icosahedra, 90 vertices and 225 tetrahedra. This fragment corresponds to the closed helix of 15 icosahedra in the 4D {3, 3, 5} polytope. The primitive cubic lattice of these icosahedral helices envelopes not only all atoms of β-Mn, but also all tetrahedra belonging to the tiling of the β-Mn structure. The 2D projection of all atomic positions in the β-Mn unit cells shows that they are situated (by neglecting small differences) on three circumferences containing 2D projections of 90 vertices of the {3, 3, 5} polytope on the same plane. Non-crystallographic symmetry of the β-Mn crystal is defined by mapping the closed icosahedral helix of the {3, 3, 5} polytope into 3D Euclidean space E 3. This interpretation must be correlated also with the known previous determination of non-crystallographic symmetry of the β-Mn crystal by mapping into the 3D E 3 space system of icosahedra from the 6D cubic B 6 lattice. The recently proposed determination of non-crystallographic symmetry of the β-Mn crystal actually uses the symmetries of the 8D E 8 lattice, in which both the 4D {3, 3, 5} polytope and cubic 6D B 6 lattice can be inserted.

Beschreibung: In the molecular structure of the title compound, C20H21N3O7, the quinoline ring system is slightly bent, with a dihedral angle between the phenyl and the pyridine rings of 3.47 (7)°. In the crystal, corrugated layers of molecules extending along the ab plane are generated by C—H...O hydrogen bonds. The intermolecular interactions were quantified by Hirshfeld surface analysis and two-dimensional fingerprint plots. The most significant contributions to the crystal packing are from H...H (42.3%), H...O/O...H (34.5%) and H...C/ C...H (17.6%) contacts. Molecular orbital calculations providing electron-density plots of the HOMO and LUMO as well as molecular electrostatic potentials (MEP) were computed, both with the DFT/B3LYP/6–311 G++(d,p) basis set. A molecular docking study between the title molecule and the COVID-19 main protease (PDB ID: 6LU7) was performed, showing that it is a good agent because of its affinity and ability to adhere to the active sites of the protein.

Beschreibung: In the crystal structure of the title compound, [Cu4Cl6O(C13H9N)4]·CH2Cl2, the core molecular structure consists of a Cu4 tetrahedron with a central interstitial O atom. Each edge of the Cu4 tetrahedron is bridged by a chlorido ligand. Each copper(II) cation is coordinated to the central O atom, two chlorido ligands and one N atom of the 4-phenylethynylpyridine ligand. In the crystal, the molecules are linked by intermolecular C—H...Cl interactions. Furthermore, C—H...π and π–π interactions also connect the molecules, forming a three-dimensional network. Hirshfeld surface analysis indicates that the most important contributions for the packing arrangement are from H...H and C...H/H...C interactions.

Beschreibung: At 100 K, the title compound, C13H12N2O2, crystallizes in the orthorhombic space group Pna21 with two very similar molecules in the asymmetric unit. An intramolecular N—H...O hydrogen bond leads to an S(6) graph-set motif in each of the molecules. Intermolecular π–π stacking and C=O...π interactions involving the aldehyde O atoms link molecules into stacks parallel to [100]. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing stem from H...H (49.4%) and H...O/O...H (21.5%) interactions. Energy framework calculations reveal a significant contribution of dispersion energy. The crystal studied was refined as a two-component inversion twin.

Beschreibung: Co-crystallization from methanol of 3-amino-1H-pyrazole with 3,5-dinitrobenzoic acid produces 3-amino-1H-pyrazol-2-ium 3,5-dinitrobenzoate monohydrate, C3H6N3 +·C7H3N2O6 −·H2O, (I), while similar co-crystallization of this pyrazole with an equimolar quantity of fumaric acid produces bis(3-amino-1H-pyrazol-2-ium) fumarate–fumaric acid (1/1), 2C3H6N3 +·C4H2O4 2−·C4H4O4, (II). The reaction of 3-amino-1H-pyrazole with a dilute solution of nitric acid in methanol yields a second, orthorhombic polymorph of 3-amino-1H-pyrazol-2-ium nitrate, C3H6N3 +·NO3 −, (III). In each of (I)–(III), the bond distances in the cation provide evidence for extensive delocalization of the positive charge. In each of (I) and (II), an extensive series of O—H...O and N—H...O hydrogen bonds links the components into complex sheets, while in the structure of (III), the ions are linked by multiple N—H...O hydrogen bonds into a three-dimensional arrangement. Comparisons are made with the structures of some related compounds.

Beschreibung: Synchrotron serial crystallography (SSX) is an emerging data-collection method for micro-crystallography on synchrotron macromolecular (MX) crystallography beamlines. At SPring-8, the feasibility of the fixed-target approach was examined by collecting data using a 2D raster scan combined with goniometer rotation. Results at cryogenic temperatures demonstrated that rotation is effective for efficient data collection in SSX and the method was named serial synchrotron rotation crystallography (SS-ROX). To use this method for room-temperature (RT) data collection, a humid air and glue-coating (HAG) method was developed in which data were collected from polyvinyl alcohol-coated microcrystals fixed on a loop under humidity-controlled air. The performance and the RT data-collection strategy for micro-crystallography were evaluated using microcrystals of lysozyme. Although a change in unit-cell dimensions of up to 1% was observed during data collection, the impact on data quality was marginal. A comparison of data obtained at various absorbed doses revealed that absorbed doses of up to 210 kGy were tolerable in both global and local damage. Although this limits the number of photons deposited on each crystal, increasing the number of merged images improved the resolution. On the basis of these results, an equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.

Beschreibung: AGAP1 is often considered to regulate membrane trafficking, protein transport and actin cytoskeleton dynamics. Recent studies have shown that aberrant expression of AGAP1 is associated with many diseases, including neurodevelopmental disorders and acute lymphoblastic leukemia. It has been proposed that the GTP-binding protein-like domain (GLD) is involved in the binding of cofactors and thus regulates the catalytic activity of AGAP1. To obtain a better understanding of the pathogenic mechanism underpinning AGAP1-related diseases, it is essential to obtain structural information. Here, the GLD (residues 70–235) of AGAP1 was overexpressed in Escherichia coli BL21 (DE3) cells. Affinity and gel-filtration chromatography were used to obtain AGAP1GLD with high purity for crystallization. Using the hanging-drop vapor-diffusion method with the protein at a final concentration of 20 mg ml−1, AGAP1GLD protein crystals of suitable size were obtained. The crystals were found to diffract to 3.0 Å resolution and belonged to space group I4, with unit-cell parameters a = 100.39, b = 100.39, c = 48.08 Å. The structure of AGAP1GLD exhibits the highly conserved functional G1–G5 loops and is generally similar to other characterized ADP-ribosylation factor (Arf) GTPase-activating proteins (GAPs), implying an analogous function to Arf GAPs. Additionally, this study indicates that AGAP1 could be classified as a type of NTPase, the activity of which might be regulated by protein partners or by its other domains. Taken together, these results provide insight into the regulatory mechanisms of AGAP1 in cell signaling.

Beschreibung: A novel member of the family 3 carbohydrate-binding modules (CBM3s) is encoded by a gene (Cthe_0271) in Clostridium thermocellum which is the most highly expressed gene in the bacterium during its growth on several types of biomass substrates. Surprisingly, CtCBM3-0271 binds to at least two different types of xylan, instead of the common binding of CBM3s to cellulosic substrates. CtCBM3-0271 was crystallized and its three-dimensional structure was solved and refined to a resolution of 1.8 Å. In order to learn more about the role of this type of CBM3, a comparative study with its orthologue from Clostridium clariflavum (encoded by the Clocl_1192 gene) was performed, and the three-dimensional structure of CcCBM3-1192 was determined to 1.6 Å resolution. Carbohydrate binding by CcCBM3-1192 was found to be similar to that by CtCBM3-0271; both exhibited binding to xylan rather than to cellulose. Comparative structural analysis of the two CBM3s provided a clear functional correlation of structure and binding, in which the two CBM3s lack the required number of binding residues in their cellulose-binding strips and thus lack cellulose-binding capabilities. This is an enigma, as CtCBM3-0271 was reported to be a highly expressed protein when the bacterium was grown on cellulose. An additional unexpected finding was that CcCBM3-1192 does not contain the calcium ion that was considered to play a structural stabilizing role in the CBM3 family. Despite the lack of calcium, the five residues that form the calcium-binding site are conserved. The absence of calcium results in conformational changes in two loops of the CcCBM3-1192 structure. In this context, superposition of the non-calcium-binding CcCBM3-1192 with CtCBM3-0271 and other calcium-binding CBM3s reveals a much broader two-loop region in the former compared with CtCBM3-0271.

Beschreibung: The crystal structures of two single-enantiomer amidophosphoesters with an (O)2P(O)(N) skeleton and one single-enantiomer phosphoric triamide with an (N)2P(O)(N) skeleton were studied. The compounds are diphenyl [(R)-(+)-α-4-dimethylbenzylamido]phosphate, (I), and diphenyl [(S)-(−)-α-4-dimethylbenzylamido]phosphate, (II), both C21H22NO3P, and N-(2,6-difluorobenzoyl)-N′,N′′-bis[(R)-(+)-α-ethylbenzyl]phosphoric triamide, C25H28F2N3O2P, (III). The asymmetric units contain two amidophosphoester molecules for (I) and (II), and one phosphoric triamide molecule for (III). In the crystal structures of (I) and (II), molecules are assembled in a similar one-dimensional chiral ribbon architecture, but with almost a mirror-image relationship with respect to each other through N—H...O(P) and C—H...O(P) hydrogen bonds along [010]. In the crystal structure of (III), the chiral tape architecture along [100] is mediated by N—H...O(P) and N—H...O(C) hydrogen bonds, and the tapes are connected into slabs by C—H...O interactions (along the ab plane). The differences/similarities of the two diastereotopic phenoxy groups in (I)/(II) and the two chiral amine fragments in (III) were studied on the grounds of geometry, conformation and contribution to the crystal packing, as well as 1H and 13C signals in a solution NMR study.

Beschreibung: Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

Beschreibung: In the article by Li et al. [Acta Cryst. (2007), E63, m2536], four imidazole H atoms are missing in the refinement.

Beschreibung: The structure of tris(ethane-1,2-diamine-κ2 N,N')cobalt(III) bis(iodide) triiodide, [Co(C2H8N2)3]I3(I)2, at 120 K has orthorhombic (P212121) symmetry. The diamine nitrogen atoms form N—H...I hydrogen bonds throughout the lattice, resulting in a three-dimensional network, which involves the iodide and all atoms in the triiodide anions.

Beschreibung: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite-type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower-symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non-existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.

Beschreibung: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front-runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.

Beschreibung: The crystal structure of the title complex, cis-[Cr(NCS)2(cyclam)]Br (cyclam = 1,4,8,11-tetraazacyclotetradecane, C10H24N4), has been determined from synchrotron X-ray data. The asymmetric unit contains one [Cr(NCS)2(cyclam)]+ cation and one bromide anion. The CrIII ion of the complex cation is coordinated by the four N atoms of the cyclam ligand and by two N-coordinating NCS groups in a cis arrangement, displaying a distorted octahedral coordination sphere. The Cr—N(cyclam) bond lengths are in the range 2.075 (3) to 2.081 (3) Å while the average Cr—N(NCS) bond length is 1.996 (16) Å. The macrocyclic cyclam moiety adopts the most stable cis-V conformation. The crystal structure is stabilized by intermolecular hydrogen bonds involving the cyclam N—H groups as donor groups, and the bromide anion and the S atom of one of the NCS ligands as acceptor groups.

Beschreibung: The title IrIII complex, [Ir(C11H8N)2Cl(C25H22P2)], was synthesized from the substitution reaction between the (ppy)2Ir(μ-Cl)2Ir(ppy)2 (ppy = deprotonated 2-phenylpyridine, C11H8N−) dimer and 1,1-bis(diphenylphosphanyl)methane (dppm, C25H22P2) under an argon gas atmosphere for 20 h. The IrIII atom is coordinated by two C,N-bidentate ppy anions, a unidentate dppm ligand and a chloride anion in a distorted octahedral IrC2N2PCl arrangement. The N donor atoms of the ppy ligands are mutually trans while the C atoms are cis. Intramolecular aromatic π–π stacking between the phenyl rings of ppy and dppm, and C—H...Cl interactions are observed. In the crystal, C—H...Cl and C—H...π contacts link the molecules into a three-dimensional network. A Hirshfeld surface analysis was carried out to further quantify the intermolecular interactions, and indicated that H...H contacts (63.9%) dominate the packing.

Beschreibung: In the title molecular salt, C26H24N3S+·Br−, the dihedral angles between the thiazole ring and its attached phenyl and benzoyl rings are 54.81 (7) and 85.51 (7)°, respectively. In the crystal, ion pairs are linked by C—H...Br and N—H...Br hydrogen bonds and are connected into helical chains extending along the c-axis direction by weak, electrostatic S...Br− interactions. A Hirshfeld surface analysis was performed, which showed the dominant role of H...H contacts (51.3%).

Beschreibung: Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excised via the spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct of Chaetomium thermophilum Prp2 was crystallized in the presence of ADP-BeF3 − and a poly-U12 RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3 −- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.

Beschreibung: Kinesin-binding protein (KBP) is an important selective inhibitor of specific kinesin family members and its genetic disruption causes Goldberg–Shprintzen syndrome. Cryo-electron microscopy (cryo-EM) has recently been used to reveal the structure of KBP alone (72 kDa) and in complex with the motor domain of the mitotic kinesin-12 KIF15 (110 kDa). KBP is an α-solenoid, tetratricopeptide-repeat protein that interacts with the microtubule-binding region of the kinesin motor domain and blocks microtubule attachment. Numerous challenges arose relating to the behavior of KBP and KBP–kinesin complexes during cryo-EM sample preparation. These included the partial denaturation of KBP by air–water interfaces, protein aggregation resulting from carbon interaction and preferential orientation. Sample preparation with a graphene oxide substrate enabled the eventual structure determination. Here, experiences with preparing these samples are detailed, bringing attention to some of the challenges and opportunities that are likely to arise from protein-surface interactions.

Beschreibung: Cryo electron microscopy (cryo-EM) can produce maps of macromolecules that have resolutions that are sufficiently high that structural details such as chemical modifications, water molecules and bound metal ions can be discerned. However, those accustomed to interpreting the electron-density maps of macromolecules produced by X-ray crystallography need to be careful when assigning features such as these in cryo-EM maps because cations, for example, interact far more strongly with electrons than they do with X-rays. Using simulated electrostatic potential (ESP) maps as a tool led us to re-examine a recent cryo-EM map of the human ribosome, and we realized that some of the ESP peaks originally identified as novel groups covalently bonded to the N7, O6 or O4 atoms of several guanines, adenines or uridines, respectively, in this structure are likely to instead represent Mg2+ ions coordinated to these atoms, which provide only partial charge compensation compared with Mg2+ ions located next to phosphate groups. In addition, direct evidence is provided for a variation in the level of 2′-O ribose methylation of nucleotides in the human ribosome. ESP maps can thus help in identifying ions next to nucleotide bases, i.e. at positions that can be difficult to address in cryo-EM maps due to charge effects, which are specifically encountered in cryo-EM. This work is particularly relevant to nucleoprotein complexes and shows that it is important to consider charge effects when interpreting cryo-EM maps, thus opening possibilities for localizing charges in structures that may be relevant for enzymatic mechanisms and drug interactions.

Beschreibung: The canonical O-mannosylation pathway in humans is essential for the functional glycosylation of α-dystroglycan. Disruption of this post-translational modification pathway leads to congenital muscular dystrophies. The first committed step in the construction of a functional matriglycan structure involves the post-translational modification of α-dystroglycan. This is essential for binding extracellular matrix proteins and arenaviruses, and is catalyzed by β-1,4-N-acetylglucosaminyltransferase 2 (POMGNT2). While another glycosyl transferase, β-1,4-N-acetylglucosaminyltransferase 1 (POMGNT1), has been shown to be promiscuous in extending O-mannosylated sites, POMGNT2 has been shown to display significant primary amino-acid selectivity near the site of O-mannosylation. Moreover, several single point mutations in POMGNT2 have been identified in patients with assorted dystroglycanopathies such as Walker–Warburg syndrome and limb girdle muscular dystrophy. To gain insight into POMGNT2 function in humans, the enzyme was expressed as a soluble, secreted fusion protein by transient infection of HEK293 suspension cultures. Here, crystal structures of POMGNT2 (amino-acid residues 25–580) with and without UDP bound are reported. Consistent with a novel fold and a unique domain organization, no molecular-replacement model was available and phases were obtained through crystallization of a selenomethionine variant of the enzyme in the same space group. Tetragonal (space group P4212; unit-cell parameters a = b = 129.8, c = 81.6 Å, α = γ = β = 90°) crystals with UDP bound diffracted to 1.98 Å resolution and contained a single monomer in the asymmetric unit. Orthorhombic (space group P212121; unit-cell parameters a = 142.3, b = 153.9, c = 187.4 Å, α = γ = β = 90°) crystals were also obtained; they diffracted to 2.57 Å resolution and contained four monomers with differential glycosylation patterns and conformations. These structures provide the first rational basis for an explanation of the loss-of-function mutations and offer significant insights into the mechanics of this important human enzyme.

Beschreibung: Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.

Beschreibung: The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

Beschreibung: The crystal structures of five new salts of 2-chloro-4-nitroaniline (2Cl4na) and 2-methyl-6-nitroaniline (2m6na) with inorganic acids, namely, 2-chloro-4-nitroanilinium bromide, C6H6ClN2O2 +·Br− (1), 2-chloro-4-nitroanilinium hydrogen sulfate, C6H6ClN2O2 +·HSO4 − (2), 2-methyl-6-nitroanilinium bromide, C7H9N2O2 +·Br− (3), 2-methyl-6-nitroanilinium triiodide, C7H9N2O2 +·I3 − (4), and 2-methyl-6-nitroanilinium hydrogen sulfate, C7H9N2O2 +·HSO4 − (5), were determined by single-crystal X-ray diffraction. Theoretical calculations of the relaxed potential energy surface (rPES) revealed that the energy barriers for the rotation of the nitro group for isolated H2Cl4na+ and H2m6na+ cations are 4.6 and 11.6 kcal mol−1, respectively. The ammonium group and respective anions form hydrogen bonds which are the most important interactions and are arranged in zero- (in 3), one- (in 1 and 4) or two-dimensional (in 2 and 5) networks. Hydrogen-bonding patterns were analyzed by means of mathematical relationships between graph-set descriptors and compared with previously reported nitroaniline salts. Hirshfeld surface analysis indicates that the nitro group plays a dominant role among the weak interactions, i.e. C—H...O(NO2), NO2...π(Ar) and O(NO2)...π(NO2). The frequency of the νsNO2 vibration is correlated with the type of interaction in which the NO2 group is involved. Analysis of the νsNO2 band observed in the IR and Raman spectra allowed an assessment of its shift in the sequence (H2m6na)I3 (4) 〈 (H2m6na)HSO4 (5) 〈 (H2m6na)Br (3) 〈 (H2Cl4na)Br (1) 〈 (H2Cl4na)HSO4 (2).

Beschreibung: New syntheses have been developed for the synthesis of (borohydrido-κ3 H)tris[η5-(trimethylsilyl)cyclopentadienyl]uranium(IV), [U(BH4)(C8H13Si)3] or Cp′3U(BH4) (Cp′ = C5H4SiMe3) and its structure has been determined by single-crystal X-ray crystallography. This compound crystallized in the space group Poverline{1} and the structure features three η 5-coordinated Cp′ rings and a κ 3-coordinated (BH4)− ligand.

Beschreibung: The coordination properties of four hydroxypyridinecarboxylates, designed for the treatment of iron-overloading conditions as bidentate O,O′-donor ligands, have been studied with ZnII in the solid state. The coordination compounds [Zn(A1)2(H2O)2] (1), [Zn(A2)2(H2O)] (2), [Zn(A3)2(H2O)]·2H2O (3) and [Zn2(B1)4(H2O)2]·4H2O (4), where the ligands are 1-methyl-4-oxidopyridinium-3-carboxylate (A1, C7H6NO3), 1,6-dimethyl-4-oxidopyridinium-3-carboxylate (A2, C8H8NO3), 1,5-dimethyl-4-oxido-pyridinium-3-carboxylate (A3, C8H8NO3) and 1-methyl-3-oxidopyridinium-4-carboxylate (B1, C7H6NO3), have been synthesized and analysed by single-crystal X-ray diffraction. The ligands were chosen to probe (i) the electronic effects of inverting the positions of the O-atom donor groups (i.e. A1 versus B1) and (ii) the electronic and steric effects of the addition of a second methyl group in different positions on the pyridine ring. Two axially coordinated water molecules resulting in a six-coordinated symmetrical octahedron complement the bis-ligand complex of A1. Ligands A2 and A3 form five-coordinated trigonal bipyramidal complexes with one additional water molecule in the coordination sphere, which is a rarely reported geometry for ZnII complexes. Ligand B1 shows a dimeric structure, where the two Zn2+ dications have slightly distorted octahedral geometry and the pyridinolate O atom of the neighbouring complex bridges them. The coordination spheres of the Zn2+ dications and the supramolecular structures are discussed in detail. The packing arrangements of 1–3 are similar, having alternating hydrophilic and hydrophobic layers, however the similarity is broken in 4. The obtained coordination geometries are compared with their previously determined CuII analogues. The study of the individual complexes is complemented with a comprehensive analysis of ZnII complexes with oxygen donor ligands with data from the Cambridge Structural Database.

Beschreibung: The synthesis and characterization of a new aluminophosphate, Na6[Al3P5O20], obtained as single crystals in the same experiment together with Cl-sodalite, Na8[Al6Si6O24]Cl2, is reported. Na6[Al3P5O20], with a strongly pseudo-orthorhombic lattice, is described by the monoclinic crystal structure established in the study of a pseudomerohedric microtwin. The design of Na6[Al3P5O20] can be interpreted as an alternative to sodalite, with a monoclinic (pseudo-orthorhombic) 2×4×1 super-structure and unit-cell parameters multiples of those of sodalite: a ≃ 2a s, b ≃ 4b s and c ≃ c s. The triperiodic framework is built by AlO6, AlO4 and PO4 polyhedra having vertex-bridging contacts. While all the oxygen vertices of the Al-centred octahedra and tetrahedra are shared with phosphate groups, some of the PO4 tetrahedra remain `pendant', e.g. containing vertices not shared with other polyhedra of the aluminophosphate construction. Na atoms occupy framework channels and cavities surrounded by eight-, six- and four-membered windows with maximal effective pore widths of 4.86 × 3.24 and 4.31 × 3.18 Å. The generalized framework density is equal to 19.8, which means that the compound may be classified as a microporous zeolite. The Na6[Al3P5O20] crystal structure is discussed as being formed from octahedral rods arranged in two perpendicular directions, similar to the rods elongated in one direction in the NASICON-type compounds, which have been intensively investigated as promising materials for batteries. Analogous properties can be expected for phases with a modified composition of the Na6Al3P5O20 topology, where the Al atoms at the centres of octahedra are replaced by Fe, V or Cr.

Beschreibung: The magnetic structure in Er3Cu4Sn4 has been determined using high-resolution powder neutron diffraction, supported by symmetry analysis. At low temperatures, Er3Cu4Sn4 assumes a crystal structure of the Tm3Cu4Sn4 type (in the monoclinic space group C2/m). The Er atoms occupy two distinct Wyckoff sites: 2c and 4i. It has been found that the Er magnetic moments on the 2c site form a commensurate antiferromagnetic structure (k 1 = [0, 0, ½]) below 6 K. The magnetic moments reach 8.91 (8) μB at 1.4 K and are parallel to the b axis. The Er magnetic moments on the 4i site order below 2 K and form an incommensurate antiferromagnetic sine-modulated structure (k 2 = [1, 0.4667 (1), ½]), with magnetic moments lying in the ac plane and perpendicular to the a axis. The amplitude of modulation equals 8.7 (1) μB at 1.4 K.

Beschreibung: Scipion is a modular image-processing framework that integrates several software packages under a unified interface while taking care of file formats and conversions. Here, new developments and capabilities of the Scipion plugin for the widely used RELION software package are presented and illustrated with an image-processing pipeline for published data. The user interfaces of Scipion and RELION are compared and the key differences are highlighted, allowing this manuscript to be used as a guide for both new and experienced users of this software. Different on-the-fly image-processing options are also discussed, demonstrating the flexibility of the Scipion framework.

Beschreibung: Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.

Beschreibung: Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thorn et al. (2017), Acta Cryst. D73, 729–727], a revised metric is defined for detecting ice from deposited protein structure-factor data, and this metric is validated using full-frame diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography. Using this revised metric and improved algorithms, an analysis of structure-factor data from a random sample of 89 827 PDB entries collected at cryogenic temperatures indicates that roughly 16% show evidence of ice contamination, and that this fraction increases with increasing solvent content and maximum solvent-cavity size. By examining the ice diffraction-peak positions at which structure-factor perturbations are observed, it is found that roughly 25% of crystals exhibit ice with primarily hexagonal character, indicating that inadequate cooling rates and/or cryoprotectant concentrations were used, while the remaining 75% show ice with a stacking-disordered or cubic character.

Beschreibung: In this paper, several approaches to be used to accelerate algorithms for fitting an atomic structure into a given 3D density map determined by cryo-EM are discussed. Rotation and translation of the atomic structure to find similarity scores are used and implemented with discrete Fourier transforms. Several rotations can be combined into groups to accelerate processing. The finite resolution of experimental and simulated maps allows a reduction in the number of rotations and translations needed in order to estimate similarity-score values.

Beschreibung: The reaction of Co(NCS)2 with 3-(aminomethyl)pyridine as coligand leads to the formation of crystals of the title compound, [Co(NCS)2(C6H8N2)2] n , that were characterized by single-crystal X-ray analysis. In the crystal structure, the CoII cations are octahedrally coordinated by two terminal N-bonded thiocyanate anions as well as two pyridine and two amino N atoms of four symmetry-equivalent 3-(aminomethyl)pyridine coligands with all pairs of equivalent atoms in a trans position. The CoII cations are linked by the 3-(aminomethyl)pyridine coligands into layers parallel to the ac plane. These layers are further linked by intermolecular N—H...S hydrogen bonding into a three-dimensional network. The purity of the title compound was determined by X-ray powder diffraction and its thermal behavior was investigated by differential scanning calorimetry and thermogravimetry.

Beschreibung: Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.

Beschreibung: Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.

Beschreibung: Biotin protein ligase catalyses the post-translational modification of biotin carboxyl carrier protein (BCCP) domains, a modification that is crucial for the function of several carboxylases. It is a two-step process that results in the covalent attachment of biotin to the ɛ-amino group of a conserved lysine of the BCCP domain of a carboxylase in an ATP-dependent manner. In Leishmania, three mitochondrial enzymes, acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, depend on biotinylation for activity. In view of the indispensable role of the biotinylating enzyme in the activation of these carboxylases, crystal structures of L. major biotin protein ligase complexed with biotin and with biotinyl-5′-AMP have been solved. L. major biotin protein ligase crystallizes as a unique dimer formed by cross-handshake interactions of the hinge region of the two monomers formed by partial unfolding of the C-terminal domain. Interestingly, the substrate (BCCP domain)-binding site of each monomer is occupied by its own C-terminal domain in the dimer structure. This was observed in all of the crystals that were obtained, suggesting a closed/inactive conformation of the enzyme. Size-exclusion chromatography studies carried out using high protein concentrations (0.5 mM) suggest the formation of a concentration-dependent dimer that exists in equilibrium with the monomer.

Beschreibung: The plant-specific class XI myosins (MyoXIs) play key roles at the molecular, cellular and tissue levels, engaging diverse adaptor proteins to transport cargoes along actin filaments. To recognize their cargoes, MyoXIs have a C-terminal globular tail domain (GTD) that is evolutionarily related to those of class V myosins (MyoVs) from animals and fungi. Despite recent advances in understanding the functional roles played by MyoXI in plants, the structure of its GTD, and therefore the molecular determinants for cargo selectivity and recognition, remain elusive. In this study, the first crystal structure of a MyoXI GTD, that of MyoXI-K from Arabidopsis thaliana, was elucidated at 2.35 Å resolution using a low-identity and fragment-based phasing approach in ARCIMBOLDO_SHREDDER. The results reveal that both the composition and the length of the α5–α6 loop are distinctive features of MyoXI-K, providing evidence for a structural stabilizing role for this loop, which is otherwise carried out by a molecular zipper in MyoV GTDs. The crystal structure also shows that most of the characterized cargo-binding sites in MyoVs are not conserved in plant MyoXIs, pointing to plant-specific cargo-recognition mechanisms. Notably, the main elements involved in the self-regulation mechanism of MyoVs are conserved in plant MyoXIs, indicating this to be an ancient ancestral trait.

Beschreibung: Specific features of the crystal chemistry of lamprophyllite-group minerals (LGMs) are discussed using the available literature data and the results of the single-crystal X-ray diffraction and a Raman spectroscopic studies of several samples taken from the Murun alkaline complex (Russia), and Rocky Boy and Gordon Butte pegmatites (USA) presented here. The studied samples are unique in their chemical features and the distribution of cations over structural sites. In particular, the sample from the Gordon Butte pegmatite is a member of the barytolamprophyllite–emmerichite solid solution series, whereas the samples from the Murun alkaline complex and from the Rocky Boy pegmatite are intermediate members of the solid solution series formed by lamprophyllite and a hypothetical Sr analogue of emmerichite. The predominance of O2− over OH− and F− at the X site is a specific feature of sample Cha-192 from the Murun alkaline complex. New data on the Raman spectra of LGMs obtained in this work show that the wavenumbers of the O—H stretching vibrations depend on the occupancies of the M2 and M3 sites coordinating with (OH)− groups. Cations other than Na+ and Ti4+ (mainly, Mg and Fe3+) can play a significant role in the coordination of the X site occupied by (OH)−. Data on polarized Raman spectra of an oriented sample indicate that the OH groups having different local coordinations have similar orientations with respect to the crystal. The calculated measures of similarity (Δ) for lamprophyllite and ericssonite are identical (0.157 and 0.077 for the 2M- and 2O-polytypes, respectively), which indicates that these minerals are crystal-chemically isotypic and probably should be considered within the same mineral group by analogy to the other mineralogical groups which combine isotypic minerals.

Beschreibung: The depth of field (DoF) was extended 2.8-fold to achieve rapid crystal screening by retrofitting a custom-designed micro-retarder array (µRA) in the optical beam path of a nonlinear optical microscope. The merits of the proposed strategy for DoF enhancement were assessed in applications of second-harmonic generation imaging of protein crystals. It was found that DoF extension increased the number of crystals detected while simultaneously reducing the number of `z-slices' required for screening. Experimental measurements of the wavelength-dependence of the extended DoF were in excellent agreement with theoretical predictions. These results provide a simple and broadly applicable approach to increase the throughput of existing nonlinear optical imaging methods for protein crystal screening.

Beschreibung: In the title molecular salt, (C6H16N2)[CoCl4], the complete dication is generated by crystallographic inversion symmetry and the piperazine ring adopts a chair conformation with the pendant methyl groups in equatorial orientations. The complete dianion is generated by crystallographic twofold symmetry. In the crystal, the (C6H16N2)2+ and [CoCl4]2− ions are linked by N—H...Cl and C—H...Cl hydrogen bonds, thereby forming a two-dimensional supramolecular network. The Hirshfeld surface analysis and fingerprint plots reveal that the largest contributions to the crystal stability come from H...Cl/Cl...H (68.4%) and H...H (27.4%) contacts.

Beschreibung: Hexagonal boron nitride (h-BN) has been generally interpreted as having an AA stacking sequence. Evidence is presented in this article indicating that typical commercial h-BN platelets (∼10–500 nm in thickness) exhibit stacks of parallel nanosheets (∼10 nm in thickness) predominantly in the AB sequence. The AB-stacked nanosheet occurs as a metastable phase of h-BN resulting from the preferred texture and lateral growth of armchair (110) planes. It appears as an independent nanosheet or unit for h-BN platelets. The analysis is supported by simulation of thin AB films (2–20 layers), which explains the unique X-ray diffraction pattern of h-BN. With this analysis and the role of pressure in commercial high-pressure high-temperature sintering (driving nucleation and parallelizing the in-plane crystalline growth of the nuclei), a growth mechanism is proposed for 2D h-BN (on a substrate) as `substrate-induced 2D growth', where the substrate plays the role of pressure.

Beschreibung: The novel π-coordination compound [CuI(m-dmphast)NO3], where m-dmphast = 5-(allylthio)-1-(3,5-dimethylphenyl)-1H-tetrazole, is characterized using single-crystal X-ray diffraction and crystallizes in a noncentrosymmetric space group. Additionally, for the first time in this group of materials, the streaks of X-ray diffuse scattering in the reciprocal space sections were observed and described. This gave the possibility for a deeper insight into the local structure of the title compound. The conjecture about the origin of diffuse scattering was derived from average structure solution. It was then confirmed using the local structure modelling. The extended [Cu(m-dmphast)NO3]∞ chains, connected by weak interactions, produce layers which can exist in two enantiomeric forms, one of which predominates.

Beschreibung: Single crystals of (E)-N′-(4-isopropylbenzylidene)isonicotinohydrazide monohydrate (IBIHM) were grown from ethanol by the slow evaporation from solution growth technique at room temperature. The structure was elucidated by single-crystal X-ray diffraction analysis and crystallized in the orthorhombic system with noncentrosymmetric space group P212121. Optical studies reveal that the absorption was minimum in the visible region and the band-gap energy was estimated using the Kubelka–Munk algorithm. The functional groups were identified by Fourier transform infrared spectral analysis. A scanning electron microscopy study revealed the surface morphology of the grown crystal. Investigation of the intermolecular interactions, crystal packing using Hirshfeld surface analysis and single-crystal X-ray diffraction confirm that the close contacts were associated with molecular interactions. Fingerprint plots of Hirshfeld surfaces are used to locate and analyze the percentage of hydrogen-bonding interactions. The second-harmonic generation efficiency of the grown specimen was superior to that of the reference material, potassium dihydrogen phosphate. The grown crystals were further characterized by mass spectrometry and elemental analysis. Theoretical studies using density functional theory (DFT) greatly substantiated the experimental observations. Large first-order molecular hyperpolarizability (β) of about ∼70× was observed for IBIHM. The efficiency of IBIHM in terms of nonlinear optical response was verified and the molecule displayed greater chemical stability and reactivity.

Beschreibung: In the title compound, C25H22N2O3S·0.04H2O, the central cyclohexane ring adopts a chair conformation. In the crystal, molecules are linked by N—H...O, C—H...O, and C—H...N hydrogen bonds, forming the molecular layers parallel to the bc plane, which interact by the van der Waals forces between them. A Hirshfeld surface analysis indicates that the contributions from the most prevalent interactions are H...H (41.2%), C...H/H...C (20.3%), O...H/H...O (17.8%) and N...H/H...N (10.6%).

Beschreibung: The digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21 am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.

Beschreibung: Equation (16) and some entries in Table 1 in the article by Scardi & Leoni [(2001), Acta Cryst. A57, 604–613] are corrected.

Beschreibung: The cadherin superfamily of calcium-dependent cell-adhesion proteins has over 100 members in the human genome. All members of the superfamily feature at least a pair of extracellular cadherin (EC) repeats with calcium-binding sites in the EC linker region. The EC repeats across family members form distinct complexes that mediate cellular adhesion. For instance, classical cadherins (five EC repeats) strand-swap their N-termini and exchange tryptophan residues in EC1, while the clustered protocadherins (six EC repeats) use an extended antiparallel `forearm handshake' involving repeats EC1–EC4. The 7D-cadherins, cadherin-16 (CDH16) and cadherin-17 (CDH17), are the most similar to classical cadherins and have seven EC repeats, two of which are likely to have arisen from gene duplication of EC1–2 from a classical ancestor. However, CDH16 and CDH17 lack the EC1 tryptophan residue used by classical cadherins to mediate adhesion. The structure of human CDH17 EC1–2 presented here reveals features that are not seen in classical cadherins and that are incompatible with the EC1 strand-swap mechanism for adhesion. Analyses of crystal contacts, predicted glycosylation and disease-related mutations are presented along with sequence alignments suggesting that the novel features in the CDH17 EC1–2 structure are well conserved. These results hint at distinct adhesive properties for 7D-cadherins.

Beschreibung: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal-binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine-dependent inhibitor compounds.

Beschreibung: In the title compounds C23H21ClN2O3 [I, namely 1-(4-chlorophenyl)-4-(4-methylphenyl)-3,8-dioxo-1,2,5,6,7,8-hexahydroquine-3-carboxylic acid] and C24H22N2O3 [II, namely 4-(4-methoxyphenyl)-1-(4-methylphenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile], each of the cyclohexene and dihydropyridine rings of the 1,2,5,6,7,8-hexahydroquinoline moieties adopts a twisted-boat conformation. The asymmetric units of both compounds I and II consist of two independent molecules (A and B). In II A, three carbon atoms of the cyclohexene ring are disordered over two sets of sites in a 0.670 (11):0.330 (11) occupancy ratio. In the crystal of I, molecules are linked through classical N—H...O hydrogen bonds, forming inversion dimers with an R 2 2(8) ring motif and with their molecular planes parallel to the crystallographic (020) plane. Non-classical C—H...O hydrogen-bonding interactions connect the dimers, resulting in a three-dimensional network. In the crystal of II, molecules are linked by C—H...N, C—H...O and C—H...π interactions, forming a three-dimensional network.

Beschreibung: In the title compound, C33H26N4O4, the two fused five-membered rings and their N-bound aromatic substituents form a pincer-like motif. The relative conformations about the three chiral carbon atoms are established. In the crystal, a combination of C—H...O and C—H...N hydrogen bonds and C—H...π(ring) interactions leads to the formation of layers parallel to the bc plane. A Hirshfeld surface analysis indicates that the most significant contributions to the crystal packing are from H...H (44.3%), C...H/H...C (29.8%) and O...H/H...O (15.0%) contacts.

Beschreibung: Single crystals of Ni3Se2 (trinickel diselenide) and NiSe (nickel selenide) with stoichiometric chemical compositions were grown in evacuated silica-glass tubes. The chemical compositions of the single crystals of Ni3Se2 and NiSe were determined by scanning electron microscopy and energy-dispersive X-ray spectroscopy (SEM/EDS). The crystal structures of Ni3Se2 [rhombohedral, space group R32, a = 6.02813 (13), c = 7.24883 (16) Å, Z = 3] and NiSe [hexagonal, space group P63/mmc, a = 3.66147 (10), c = 5.35766 (16) Å, Z = 2] were analyzed by single-crystal X-ray diffraction and refined to yield R values of 0.020 and 0.018 for 117 and 85 unique reflections, respectively, with F o 〉 4σ(F o). R32 is a Sohncke type of space group where enantiomeric structures can exist; the single-domain structure obtained by the refinement was confirmed to be correct by a Flack parameter of −0.05 (2). The existence of Ni—Ni bonds was confirmed in both compounds, in addition to the Ni—Se bonds. The value of the atomic displacement parameter (mean-square displacement) of each atom in NiSe was larger than that in Ni3Se2. The larger amplitude of the atoms in NiSe corresponds to longer Ni—Se and Ni—Ni bond lengths in NiSe than in Ni3Se2. The Debye temperatures, θD, estimated from observed mean-square displacements for Ni and Se in Ni3Se2, were 322 and 298 K, respectively, while those for Ni and Se in NiSe were 246 and 241 K, respectively. The existence of large cavities in the structure and the weak bonding force are likely responsible for the brittle and soft nature of the NiSe crystal.

Beschreibung: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6–4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle.

Beschreibung: The crystal structures of three intermediate compounds in the synthesis of 8-bromo-2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin are reported; 4-bromo-2-formyl-1-tosyl-1H-pyrrole, C12H10BrNO3S, (E)-4-bromo-2-(2-nitrovinyl)-1-tosyl-1H-pyrrole, C13H11BrN2O4S, and 6-(4-bromo-1-tosylpyrrol-2-yl)-4,4-dimethyl-5-nitrohexan-2-one, C19H23BrN2O5S. The compounds show multitudinous intermolecular C—H...O interactions, with bond distances and angle consistent in the series and within expectations, as well as varied packing types. The merits of collecting data beyond the standard resolution usually reported for small molecules are discussed.

Beschreibung: In the title compound, C24H20ClNO2, the mean planes of 4-chlorophenyl, 2-methylphenyl and phenylene rings make dihedral angles of 62.8 (2), 65.1 (3) and 15.1 (2)°, respectively, with the 5-methyl-1,2-oxazole ring. In the crystal, molecules are linked by intermolecular C—H...N, C—H...Cl, C—H...π contacts and π–π stacking interactions between the phenylene groups. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (48.7%), H...C/C...H (22.2%), Cl...H/H...Cl (8.8%), H...O/O...H (8.2%) and H...N/N...H (5.1%) interactions.

Beschreibung: Cycloaddition reactions between 3-(5-aryloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(thiophen-2-yl)prop-2-en-1-ones and thiosemicarbazide leads to the formation of reduced 3,4′-bipyrazole-2-carbothioamides. Further cycloaddition of these intermediates with either diethyl acetylenedicarboxylate or 4-bromophenacyl bromide leads to reduced 3,4′-bipyrazoles carrying oxothiazole or thiazole substituents, respectively. The structures of two representative intermediates and two representative products established unambiguously the regiochemistry of the cycloaddition reactions. The molecules of 3′-methyl-5′-(2-methylphenoxy)-1′-phenyl-5-(thiophen-2-yl)-3,4-dihydro-1′H,2H-3,4′-bipyrazole-2-carbothioamide, C25H23N5OS2 (Ia), are linked by N—H...N hydrogen bonds to form simple C(8) chains. The analogous compound 5′-(2,4-dichlorophenoxy)-3′-methyl-1′-phenyl-5-(thiophen-2-yl)-3,4-dihydro-1′H,2H-3,4′-bipyrazole-2-carbothioamide hemihydrate crystallizes as a hemihydrate, C24H19Cl2N5OS2·0.5H2O (Ib), and the independent components are linked into a chain of spiro-fused R 4 4(20) rings by a combination of O—H...N and N—H...O hydrogen bonds. In the structure of ethyl (Z)-2-{2-[3′-methyl-1′-phenyl-5-(thiophen-2-yl)-5′-(2-methylphenoxy)-3,4-dihydro-1′H,2H-3,4′-bipyrazole-2-yl]-4-oxo-4,5-dihydrothiazol-5-ylidene}acetate, C31H27N5O4S2 (II), inversion-related pairs of molecules are linked by paired C—H...π(arene) hydrogen bonds to form cyclic centrosymmetric dimers, but there are no direction-specific intermolecular interactions in 4-(4-bromophenyl)-2-[5′-(2,4-dichlorophenoxy)-3′-methyl-1′-phenyl-5-(thiophen-2-yl)-3,4-dihydro-1′H,2H-3,4′-bipyrazole-2-yl]-4-thiazole, C32H22BrCl2N5OS2 (III). Comparisons are made with the structures of some related compounds.

Beschreibung: We report two new variants of the X-phase (orthorhombic, space group Pnnm) derived from the Mn–Co–Ge system. Two compositionally related crystals were investigated by means of single-crystal X-ray diffraction (XRD) and energy dispersive spectroscopy (EDS). The Mn14.9Co15.5Ge6.6 and Mn14Co16.2Ge6.8 intermetallic compounds are part of the homogeneity region of the X-phase and adopt the Mn14(Mn0.11Co0.64Si0.25)23 structure type. The composition obtained from refinement of the XRD data is in agreement with the EDS results. In the present study, chemical disorder was only detected on the 8h positions. The ordering is compared with other members of the X-phase family and shows that the degree of disordering depends on the chemical composition. No completely ordered variants of the X-phase have yet been reported.

Beschreibung: The true identity of the diethyl ether adduct of tungsten(IV) chloride, WCl4(Et2O) x , has been in doubt since 1985. Initially postulated as the bis-adduct, WCl4(Et2O)2, questions arose when elemental analyses were more in line with a mono-ether adduct, viz. WCl4(Et2O). It was proposed that this was due to the thermal instability of the bis-adduct. Here, we report the room-temperature X-ray crystal structure and Hirshfeld surface characteristics of trans-tetrachloridobis(diethyl ether)tungsten(IV), trans-WCl4(Et2O)2 or trans-[WCl4(C4H10O)2]. The compound crystallizes, with half of the molecule in the asymmetric unit, in the centrosymmetric space group P21/n. The W—O distance is 2.070 (2) Å, while the W—Cl distances are 2.3586 (10) and 2.3554 (10) Å.

Beschreibung: Advances in instrumentation, as well as the development of powerful crystallographic software have significantly facilitated the collection of high-resolution diffraction data and have made X-ray powder diffraction (XRPD) particularly useful for the extraction of structural information; this is true even for complex molecules, especially when combined with synchrotron radiation. In this study, in-line with past instrumental profile studies, an improved data collection strategy exploiting the MYTHEN II detector system together with significant beam focusing and tailored data collection options was introduced and optimized for protein samples at the Material Science beamline at the Swiss Light Source. Polycrystalline precipitates of octreotide, a somatostatin analog of particular pharmaceutical interest, were examined with this novel approach. XRPD experiments resulted in high angular and d-spacing (1.87 Å) resolution data, from which electron-density maps of enhanced quality were extracted, revealing the molecule's structural properties. Since microcrystalline precipitates represent a viable alternative for administration of therapeutic macromolecules, XRPD has been acknowledged as the most applicable tool for examining a wide spectrum of physicochemical properties of such materials and performing studies ranging from phase identification to complete structural characterization.

Beschreibung: Easy crystallization distinguishes xylitol from other sugars, which usually condense into a syrup from aqueous solution. Although two polymorphs, i.e. metastable monoclinic and high-density orthorhombic, have been reported for xylitol, only the latter is in practical use. Under high pressure, the same orthorhombic phase has been obtained by both isothermal and isochoric recrystallization. The stability of the orthorhombic xylitol phase to 5.0 GPa has been correlated with a uniform compression of all hydrogen bonds and some flexibility of the molecular conformation, which cushion the pressure-induced local strains. The anisotropic compressibility of xylitol and its thermal expansion are consistent with the rule of inverse effects of pressure and temperature. This inverse strain relationship has been correlated with the dimensions and orientation of xylitol molecules in the crystal structure.

Beschreibung: The title compound, C9H7NO2S crystallizes with two independent molecules (A and B) in the asymmetric unit with Z = 8. Both molecules are almost planar with a dihedral angle between the isoxazole and thiophen rings of 3.67 (2)° in molecule A and 10.00 (1) ° in molecule B. The packing of molecules A and B is of an ABAB... type along the b-axis direction, the configuration about the C=C bond is Z. In the crystal, the presence of C—H...O, C—H... N and π–π interactions [centroid–centroid distances of 3.701 (2) and 3.766 (2) Å] link the molecules into a three-dimensional architecture. An analysis of Hirshfeld surfaces shows the importance of C—H...O and C—H...N hydrogen bonds in the packing mechanism of the crystalline structure.

Beschreibung: Sr8[Al12O24](SO4)2 (SAS) and Ca8[Al12O24](SO4)2 (CAS) are members of the aluminate sodalite-type oxides with the general chemical formula M 8[Al12O24](XO4)2 (M 2+ is the guest cation and XO4 2− is the guest anion). To discuss the role of the guest cations (M 2+ = Sr2+ and Ca2+) on the rotation of AlO4 in the oxygen tetrahedral framework in the I 43m phase, the crystal structure parameters and the probability density function of the guest ions in SAS and CAS have been investigated via synchrotron radiation X-ray powder diffraction by considering Gram–Charlier expansions. The interatomic distances between the M 2+ and O2− ions evaluated from the maximum positions in the probability density distribution are almost equal to the sum of the ideal ionic radii of the M 2+ and O2− ions. This result suggests that the geometry of the AlO4 tetrahedral framework and the fluctuation of the guest ions are mainly caused by steric effects between the M 2+ and O2− ions.

Beschreibung: When building atomic models into weak and/or low-resolution density, a common strategy is to restrain their conformation to that of a higher resolution model of the same or similar sequence. When doing so, it is important to avoid over-restraining to the reference model in the face of disagreement with the experimental data. The most common strategy for this is the use of `top-out' potentials. These act like simple harmonic restraints within a defined range, but gradually weaken when the deviation between the model and reference grows beyond that range. In each current implementation the rate at which the potential flattens at large deviations follows a fixed form, although the form chosen varies among implementations. A restraint potential with a tuneable rate of flattening would provide greater flexibility to encode the confidence in any given restraint. Here, two new such potentials are described: a Cartesian distance restraint derived from a recent generalization of common loss functions and a periodic torsion restraint based on a renormalization of the von Mises distribution. Further, their implementation as user-adjustable/switchable restraints in ISOLDE is described and their use in some real-world examples is demonstrated.

Beschreibung: Bedaquiline is one of two important new drugs for the treatment of drug-resistant tuberculosis (TB). It is marketed in the US as its fumarate salt, but only a few salts of bedaquiline have been structurally described so far. We present here five crystal structures of bedaquilinium maleate {systematic name: [4-(6-bromo-2-methoxyquinolin-3-yl)-3-hydroxy-3-(naphthalen-1-yl)-4-phenylbutyl]dimethylazanium 3-carboxyprop-2-enoate}, C32H32BrN2O2 +·C4H3O4 −, namely, a hemihydrate, a tetrahydrofuran (THF) solvate, a mixed acetone/hexane solvate, an ethyl acetate solvate, and a solvate-free structure obtained from the acetone/hexane solvate by in situ single-crystal-to-single-crystal desolvation. All salts exhibit a 1:1 cation-to-anion ratio, with the anion present as monoanionic hydromaleate and a singly protonated bedaquilinium cation. The maleate exhibits the strong intramolecular hydrogen bond typical for cis-dicarboxylic acid anions. The conformations of the cations and packing interactions in the maleate salts are compared to those of free base bedaquiline and other bedaquilinium salts.

Beschreibung: Dehydrocoupling of the adduct of dimethylamine and borane, NH(CH3)2-BH3 leads to dimethylaminoborane with formal composition N(CH3)2-BH2. The structure of this product depends on the conditions of the synthesis; it may crystallize either as a dimer in a triclinic space group forming a four-membered ring [N(CH3)2-BH2]2 or as a trimer forming a six-membered ring [N(CH3)2-BH2]3 in an orthorhombic space group. Due to the denser packing, the six-membered ring in the trimer structure should be energetically more stable than the four-membered ring. The triclinic structure is stable at low temperatures. Heating the triclinic phase above 290 K leads to a second-order phase transition to a new monoclinic polymorph. While the crystal structures of the triclinic and orthorhombic phases were already known in the literature, the monoclinic crystal structure was determined from powder diffraction data in this study. Monoclinic dimethylaminoborane crystallizes in space group C2/m with the boron and nitrogen atoms located on the mirror plane, Wyckoff position 4i, while the carbon and hydrogen atoms are on the general position 8j.

Beschreibung: xLi2O–(100 − x)TeO2 (x = 20 and 25 mol%) and xV2O5–(25 − x)Li2O–75TeO2 (x = 1, 2, 3, 4 and 5 mol%) glasses were prepared by melt-quenching and their thermal and structural properties were characterized by differential scanning calorimetry, Raman spectroscopy, high-energy X-ray diffraction and neutron diffraction and reverse Monte Carlo (RMC) simulations. The glass transition temperature increases steadily with an increase in V2O5 mol% in lithium tellurite glasses due to an increase in the average single bond energy of the glass network. The X-ray and neutron diffraction structure factors were modelled by RMC technique and the Te–O distributions show the first peak in the range 1.85–1.90 Å, with V–O = 1.75–1.95 Å, Li–O = 1.85–2.15 Å and O–O = 2.70–2.80 Å. The average Te–O coordination number decreases with an increase in Li2O mol% in lithium tellurite glasses, and the V—O coordination decreases from 5.12 to 3.81 with an increase in V2O5 concentration in vanadium lithium tellurite glasses. The O–Te–O, O–V–O, O–Li–O and O–O–O linkages have maxima in the ranges 86°–89°, 82°–87°, 80°–85° and at 59o, respectively. The structural analysis of tellurite glasses reveal significant short-range and medium-range disorder due to the existence of a wide range of Te–O and Te–Te distances in the first coordination shell.

Beschreibung: Pigment Red 52, Na2[C18H11ClN2O6S], is an industrially produced hydrazone-laked pigment. It serves as an intermediate in the synthesis of the corresponding Ca2+ and Mn2+ salts, which are used commercially for printing inks and lacquers. Hitherto, no crystal structure of any salt of Pigment Red 52 is known. Now, single crystals have been obtained of a dimethyl sulfoxide solvate hydrate of the monosodium salt of Pigment Red 52, namely, monosodium 2-[2-(3-carboxy-2-oxo-1,2-dihydronaphthalen-1-ylidene)hydrazin-1-yl]-5-chloro-4-methylbenzenesulfonate dimethyl sulfoxide monosolvate monohydrate, Na+·C18H12ClN2O6S−·H2O·C2H6OS, obtained from in-house synthesized Pigment Red 52. The crystal structure was determined by single-crystal X-ray diffraction at 173 K. In this monosodium salt, the SO3 − group is deprotonated, whereas the COOH group is protonated. The residues form chains via ionic interactions and hydrogen bonds. The chains are arranged in polar/non-polar double layers.

Beschreibung: The reaction of copper(II) sulfatepentahydrate with 2-nitrobenzoic acid and N,N,N′,N′-tetramethylethylenediamine (TMEDA) in basic solution produces the complex bis(2-nitrobenzoato-κO)(N,N,N′,N′-tetramethylethylenediamine-κ2 N,N′)copper(II), [Cu(C7H4NO4)2(C6H16N2)] or [Cu(2-nitrobenzoate)2(tmeda)]. Each carboxylate group of the 2-nitrobenzoate ligand is coordinated by CuII atom in a monodentate fashion and two TMEDA ligand nitrogen atoms are coordinate by the metal center, giving rise to a distorted square-planar coordination environment. In the crystal, metal complexes are linked by centrosymmetric C—H...O hydrogen bonds, forming ribbons via a R 2 2(10) ring motif. These ribbons are linked by further C—H...O hydrogen bonds, leading to two-dimensional hydrogen-bonded arrays parallel to the bc plane. Weak π–π stacking interactions provide additional stabilization of the crystal structure. Hirshfeld surface analysis, dnorm and two-dimensional fingerprint plots were examined to verify the contributions of the different intermolecular contacts within the supramolecular structure. The major interactions of the complex are O...H/H...O (44.9%), H...H (34%) and C...H (14.5%).

Beschreibung: The title compound, C5D6ClN2O+·Cl−, crystallizes in the orthorhombic space group, Pbcm, and consists of a 4-chloro-2-methyl-6-oxo-3,6-dihydropyrimidin-1-ium cation and a chloride anion where both moieties lie on a crystallographic mirror. The cation is disordered and was refined as two equivalent forms with occupancies of 0.750 (4)/0.250 (4), while the chloride anion is triply disordered with occupancies of 0.774 (12), 0.12 (2), and 0.11 (2). Unusually, the bond angles around the C=O unit range from 127.2 (6) to 115.2 (3)° and similar angles have been found in other structures containing a 6-oxo-3,6-dihydropyrimidin-1-ium cation, including the monclinic polymorph of the title compound, which crystallizes in the monoclinic space group P21/c [Kawai et al. (1973). Cryst. Struct. Comm. 2, 663–666]. The cations and anions pack into sheets in the ab plane linked by N—H...Cl hydrogen bonds as well as C—H...O and Cl...O interactions. In graph-set notation, these form R 3 3(11) and R 3 2(9) rings. Theoretical calculations seem to indicate that the reason for the unusual angles at the sp 2 C is the electrostatic interaction between the oxygen atom and the adjacent N—H hydrogen.

Beschreibung: The quaternary A 2W3SeO12 (A = NH4, Cs, Rb, K or Tl) selenites have been prepared in the form of single crystals by hydrothermal and novel solid-state reactions. They were characterized by X-ray diffraction, thermal and spectroscopic studies. All of them have a hexagonal tungsten oxide (HTO) related [W3SeO12]2− anionic framework with pyramidally coordinated Se4+ ions. The known A 2W3SeO12 (A = NH4, Cs or Rb) compounds are isostructural with the Cs2W3TeO12 compound and have a non-centrosymmetric layered structure containing intra-layer Se—O bonds. The new compound K2W3SeO12(α) is isostructural with the K2W3TeO12 compound and has a centrosymmetric three-dimensional structure containing interlayer Se—O bonds. It is inferred that the new Tl2W3SeO12 compound has the same three-dimensional structure as K2W3SeO12(α).

Beschreibung: The title compound, bis(N,N-diallyl-5-methoxytryptammonium) (5-MeO-DALT) fumarate (systematic name: bis{N-[2-(5-methoxy-1H-indol-3-yl)ethyl]- N-(prop-2-en-1-yl)prop-2-en-1-aminium} (E)-but-2-enedioate), 2C17H23N2O+·C4H2O4 2−, has a single tryptammonium cation and half of a fumarate dianion in the asymmetric unit. The tryptammonium and fumarate ions are held together in one-dimensional chains by a series of N—H...O hydrogen bonds. These chains are combinations of R 4 4(22) rings, and C 2 2(14) and C 4 4(28) parallel chains along [111].

Beschreibung: In the title molecule, C13H13N3O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N—H...N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (48.8%), H...C/C...H (20.9%) and H...N/N...H (19.3%) interactions. The optimized structure calculated using density functional theory at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gap is 4.9266 eV.

Beschreibung: Crystals of Cs6(SO4)3(H3PO4)4 belong to the family of alkali metal acid salts that show a high protonic conductivity at relatively low temperatures. Such properties make superprotonic crystals an excellent choice for the study of the influence of the hydrogen subsystem on the physicochemical properties and promising materials for energy-efficient technologies. Single crystals of Cs6(SO4)3(H3PO4)4 were studied by neutron diffraction methods, optical polarization microscopy, scanning electron microscopy and energy-dispersive X-ray spectroscopy. Neutron diffraction studies made it possible to determine the positions of all the atoms with high accuracy, including the H atom on a hydrogen bond characterized by a single-minimum potential, to confirm the chemical composition of the Cs6(SO4)3(H3PO4)4 crystals and their cubic symmetry in low- and high-temperature phases, and to draw conclusions about the three-dimensional system of hydrogen bonds, which is fundamentally different in comparison with other superprotonic compounds. Based on the experimental data obtained, crystal transformations with temperature changes are reported, and the stability of the chemical composition is shown.

Beschreibung: PII proteins are ubiquitous signaling proteins that are involved in the regulation of the nitrogen/carbon balance in bacteria, archaea, and some plants and algae. Signal transduction via PII proteins is modulated by effector molecules and post-translational modifications in the PII T-loop. Whereas the binding of ADP, ATP and the concomitant binding of ATP and 2-oxoglutarate (2OG) engender two distinct conformations of the T-loop that either favor or disfavor the interaction with partner proteins, the structural consequences of post-translational modifications such as phosphorylation, uridylylation and adenylylation are far less well understood. In the present study, crystal structures of the PII protein GlnK from Corynebacterium glutamicum have been determined, namely of adenylylated GlnK (adGlnK) and unmodified unadenylylated GlnK (unGlnK). AdGlnK has been proposed to act as an inducer of the transcription repressor AmtR, and the adenylylation of Tyr51 in GlnK has been proposed to be a prerequisite for this function. The structures of unGlnK and adGlnK allow the first atomic insights into the structural implications of the covalent attachment of an AMP moiety to the T-loop. The overall GlnK fold remains unaltered upon adenylylation, and T-loop adenylylation does not appear to interfere with the formation of the two major functionally important T-loop conformations, namely the extended T-loop in the canonical ADP-bound state and the compacted T-loop that is adopted upon the simultaneous binding of Mg-ATP and 2OG. Thus, the PII-typical conformational switching mechanism appears to be preserved in GlnK from C. glutamicum, while at the same time the functional repertoire becomes expanded through the accommodation of a peculiar post-translational modification.

Beschreibung: Detection of translational noncrystallographic symmetry (TNCS) can be critical for success in crystallographic phasing, particularly when molecular-replacement models are poor or anomalous phasing information is weak. If the correct TNCS is detected then expected intensity factors for each reflection can be refined, so that the maximum-likelihood functions underlying molecular replacement and single-wavelength anomalous dispersion use appropriate structure-factor normalization and variance terms. Here, an analysis of a curated database of protein structures from the Protein Data Bank to investigate how TNCS manifests in the Patterson function is described. These studies informed an algorithm for the detection of TNCS, which includes a method for detecting the number of vectors involved in any commensurate modulation (the TNCS order). The algorithm generates a ranked list of possible TNCS associations in the asymmetric unit for exploration during structure solution.

Beschreibung: A detailed understanding of the interactions between small-molecule ligands and their proposed binding targets is of the utmost importance for modern drug-development programs. Cellular retinoic acid-binding proteins I and II (CRABPI and CRABPII) facilitate a number of vital retinoid signalling pathways in mammalian cells and offer a gateway to manipulation of signalling that could potentially reduce phenotypes in serious diseases, including cancer and neurodegeneration. Although structurally very similar, the two proteins possess distinctly different biological functions, with their signalling influence being exerted through both genomic and nongenomic pathways. In this article, crystal structures are presented of the L29C mutant of Homo sapiens CRABPI in complex with naturally occurring fatty acids (1.64 Å resolution) and with the synthetic retinoid DC645 (2.41 Å resolution), and of CRABPII in complex with the ligands DC479 (1.80 Å resolution) and DC645 (1.71 Å resolution). DC645 and DC479 are two potential drug compounds identified in a recent synthetic retinoid development program. In particular, DC645 has recently been shown to have disease-modifying capabilities in neurodegenerative disease models by activating both genomic and nongenomic signalling pathways. These co-crystal structures demonstrate a canonical binding behaviour akin to that exhibited with all-trans-retinoic acid and help to explain how the compounds are able to exert an influence on part of the retinoid signalling cascade.

Beschreibung: Di-tert-butyl N,N′-{[13,15,28,30,31,33-hexaethyl-3,10,18,25,32,34-hexaazapentacyclo[25.3.1.15,8.112,16.120,23]tetratriaconta-1(31),3,5,7,9,12(33),13,15,18,20,22,24,27,29-tetradecaene-14,29-diyl]bis(methylene)}dicarbamate methanol disolvate, C52H72N8O4·2CH3OH, was found to crystallize in the space group P21/c with one half of the macrocycle (host) and one molecule of solvent (guest) in the asymmetric unit of the cell, i.e. the host molecule is located on a crystallographic symmetry center. Within the 1:2 host–guest complex, the solvent molecules are accommodated in the host cavity and held in their positions by O—H...N and N—H...O bonds, thus forming ring synthons of graph set R 2 2(7). The connection of the 1:2 host-guest complexes is accomplished by C—H...O, C—H...N and C—H...π interactions, which create a three-dimensional supramolecular network.

Beschreibung: In the title compound, C27H33NO5, a 3,3,6,6-tetramethyltetrahydroacridine-1,8-dione ring system carries an ethyl acetate substituent on the acridine N atom and an o-hydroxyphenyl ring on the central methine C atom of the dihydropyridine ring. The benzene ring is inclined to the acridine ring system at an angle of 80.45 (7)° and this conformation is stabilized by an intramolecular O—H...O hydrogen bond between the hydroxy substituent on the benzene ring and one of the carbonyl groups of the acridinedione unit. The ester C=O oxygen atom is disordered over major and minor orientations in a 0.777 (9):0.223 (9) ratio and the terminal –CH3 unit of the ethyl side chain is disordered over two sets of sites in a 0.725 (5): 0.275 (5) ratio. In the crystal, C—H...O hydrogen bonds combine to link the molecules into a three-dimensional network. van der Waals H...H contacts contribute the most to the Hirshfeld surface (66.9%) followed by O...H/H...O (22.1%) contacts associated with weak hydrogen bonds.

Beschreibung: The title compound, C24H24N2O5S, crystallizes with two independent molecules (A and B) in the asymmetric unit. In the central ring systems of both molecules, the tetrahydrofuran rings adopt envelope conformations, the pyrrolidine rings adopt a twisted-envelope conformation and the six-membered ring is in a boat conformation. In molecules A and B, the nine-membered groups attached to the central ring system are essentially planar (r.m.s. deviations of 0.002 and 0.003 Å, respectively). They form dihedral angles of 64.97 (9) and 56.06 (10)°, respectively, with the phenyl rings. In the crystal, strong intermolecular O—H...O hydrogen bonds and weak intermolecular C—H...O contacts link the molecules, forming a three-dimensional network. In addition weak π–π stacking interactions [centroid-to centroid distance = 3.7124 (13) Å] between the pyrrolidine rings of the nine-membered groups of A molecules are observed. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to quantify the intermolecular interactions present in the crystal, indicating that the environments of the two molecules are very similar. The most important contributions for the crystal packing are from H...H (55.8% for molecule A and 53.5% for molecule B), O...H/H...O (24.5% for molecule A and 26.3% for molecule B) and C...H/H...C (12.6% for molecule A and 15.7% for molecule B) interactions.

Beschreibung: A nickel(II) terephthalate complex, viz. [Ni(C6H4N2)2(H2O)4](O2CC6H4CO2)·4H2O, has been synthesized and studied by single-crystal X-ray diffraction. It crystallizes in the triclinic space group Poverline{1}. The crystal structure shows an approximately octahedral coordination environment of the complex with the [Ni(H2O)4(3-NCpy)2]2+ (3-NCpy is pyridine-3-carbonitrile) cation associated with four free water molecules and hydrogen bonded to a terephthalate dianion [graph set R 2 2(8)]. The supramolecular structure of the compound is stabilized by a three-dimensional array of O—H...O and O—H...N hydrogen bonds, along with π–π stacked pyridine-3-carbonitrile rings and C—H...O interactions.

Beschreibung: A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.

Beschreibung: In the title molecule, C16H14N2O, the dihydroquinoxaline moiety is not planar as there is a dihedral angle of 4.51 (5)° between the constituent rings. In the crystal, C—H...O hydrogen bonds form helical chains about the crystallographic 21 screw axis in the b-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (51.7%), H...C/C...H (26%) and H...O/O...H (8.5%) interactions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO–LUMO energy gap is 3.8918 eV.

Beschreibung: The title pyridazinone derivative, C19H14Cl2N2O, an important pharmacophore with a wide variety of biological applications is not planar, the chlorophenyl and pyridazinone rings being almost perpendicular, subtending a dihedral angle of 85.73 (11)°. The phenyl ring of the styryl group is coplanar with the pyridazinone ring [1.47 (12)°]. In the crystal, N—H...O hydrogen bonds form inversion dimers with an R 2 2(8) ring motif and C—H...Cl hydrogen bonds also occur. The roles of the intermolecular interactions in the crystal packing were clarified using Hirshfeld surface analysis, and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H...H (37.9%), C...H/H...C (18.7%), Cl...H/ H...Cl (16.4%) and Cl...C/C...Cl (6.7%) contacts.

Beschreibung: An algebraic approximation, of order K, of a polyhedron correlation function (CF) can be obtained from γ′′(r), its chord-length distribution (CLD), considering first, within the subinterval [D i−1, D i ] of the full range of distances, a polynomial in the two variables (r − D i−1)1/2 and (D i − r)1/2 such that its expansions around r = D i−1 and r = D i simultaneously coincide with the left and right expansions of γ′′(r) around D i−1 and D i up to the terms O(r − D i−1) K/2 and O(D i − r) K/2, respectively. Then, for each i, one integrates twice the polynomial and determines the integration constants matching the resulting integrals at the common end-points. The 3D Fourier transform of the resulting algebraic CF approximation correctly reproduces, at large q's, the asymptotic behaviour of the exact form factor up to the term O[q −(K/2+4)]. For illustration, the procedure is applied to the cube, the tetrahedron and the octahedron.

Beschreibung: In 2003, a fully automated protein crystallization and monitoring system (PXS) was developed to support the structural genomics projects that were initiated in the early 2000s. In PXS, crystallization plates were automatically set up using the vapor-diffusion method, transferred to incubators and automatically observed according to a pre-set schedule. The captured images of each crystallization drop could be monitored through the internet using a web browser. While the screening throughput of PXS was very high, the demands of users have gradually changed over the ensuing years. To study difficult proteins, it has become important to screen crystallization conditions using small amounts of proteins. Moreover, membrane proteins have become one of the main targets for X-ray crystallography. Therefore, to meet the evolving demands of users, PXS was upgraded to PXS2. In PXS2, the minimum volume of the dispenser is reduced to 0.1 µl to minimize the amount of sample, and the resolution of the captured images is increased to five million pixels in order to observe small crystallization drops in detail. In addition to the 20°C incubators, a 4°C incubator was installed in PXS2 because crystallization results may vary with temperature. To support membrane-protein crystallization, PXS2 includes a procedure for the bicelle method. In addition, the system supports a lipidic cubic phase (LCP) method that uses a film sandwich plate and that was specifically designed for PXS2. These improvements expand the applicability of PXS2, reducing the bottleneck of X-ray protein crystallography.

Beschreibung: FANCM is involved in eukaryotic DNA-damage recognition and activates the Fanconi anemia (FA) pathway through complex formation. MHF is one of the FANCM-associating components and contains a histone-fold DNA-binding domain. Loss of the FANCM–MHF interaction compromises the activation of the FA pathway, resulting in chromosomal instability. Thus, formation of the FANCM–MHF complex is important for function, but its nature largely remains elusive. Here, the aim was to reveal the molecular and structural basis for the stability of the FANCM–MHF complex. A recombinant tripartite complex containing chicken FANCM (MHF interaction region), MHF1 and MHF2 was expressed and purified. The purified tripartite complex was crystallized under various conditions and three different crystals were obtained from similar crystallization conditions. Unexpectedly, structure determination revealed that one of the crystals contained the FANCM–MHF complex but that the other two contained the MHF complex without FANCM. How FANCM dissociates from MHF was further investigated and it was found that the presence of 2-methyl-2,4-pentanediol (MPD) and an oxidative environment may have promoted its release. However, under these conditions MHF retained its complexed form. FANCM–MHF interaction involves a mixture of hydrophobic/hydrophilic interactions, and chicken FANCM contains several nonconserved cysteines within this region which may lead to aggregation with other FANCM–MHF molecules. These results indicate an unexpected nature of the FANCM–MHF complex and the data can be used to improve the stability of the complex for biochemical and structural analyses.

Beschreibung: Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays structural features in sequence space, allowing users to uncover differences between homologous structure models that can be analyzed for their relevance to chemistry or biology. LAHMA visualizes numerous structural features, also allowing one-click comparison of structure-quality plots (for example the Ramachandran plot) and `in-browser' structural visualization of 3D models.

Beschreibung: Biological macromolecules have complex three-dimensional shapes that are experimentally examined using X-ray crystallography and electron cryo-microscopy. Interpreting the data that these methods yield involves building 3D atomic models. With almost every data set, some portion of the time put into creating these models must be spent manually modifying the model in order to make it consistent with the data; this is difficult and time-consuming, in part because the data are `blurry' in three dimensions. This paper describes the design and assessment of CootVR (available at http://hamishtodd1.github.io/cvr), a prototype computer program for performing this task in virtual reality, allowing structural biologists to build molecular models into cryo-EM and crystallographic data using their hands. CootVR was timed against Coot for a very specific model-building task, and was found to give an order-of-magnitude speedup for this task. A from-scratch model build using CootVR was also attempted; from this experience it is concluded that currently CootVR does not give a speedup over Coot overall.

Beschreibung: Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, a low-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.

Beschreibung: Debio0932 is a promising lead compound in phase I clinical trials targeting the N-terminal ATP-binding pocket of the molecular chaperone heat-shock protein 90 (Hsp90N). The absence of a crystal structure of the Hsp90N–Debio0932 complex, however, has impeded further structural optimization of Debio0932 and understanding of the molecular-interaction mechanism. Here, a high-resolution crystal structure of the Hsp90N–Debio0932 complex was successfully determined (resolution limit 2.20 Å; PDB entry 6lr9) by X-ray diffraction and the molecular-interaction mechanism was analysed in detail, which suggested that Debio0932 suppresses cancer cells by accommodating itself in the ATP-binding pocket of Hsp90N, disabling its molecular-chaperone capability. The results of a thermal shift assay (ΔT m = 8.83 ± 0.90°C) and isothermal titration calorimetry (K d = 15.50 ± 1.30 nM) indicated strong binding and favourable thermodynamic changes in the binding of Hsp90N and Debio0932. Based on the crystal structure of the complex and on molecular-interaction analysis, 30 new Debio0932 derivatives were designed and nine new derivatives exhibited increased binding to Hsp90N, as determined by molecular-docking evaluation. Additionally, Debio0932 suppressed cell proliferation (IC50 values of 3.26 ± 2.82 µM for A549, 20.33 ± 5.39 µM for H1299 and 3.16 ± 1.04 µM for H1975), induced cell-cycle arrest and promoted apoptosis in three non-small-cell lung cancer (NSCLC) cell lines. These results provide novel perspectives and guidance for the development of new anti-NSCLC drugs based on the lead compound Debio0932.

Beschreibung: Apical sodium-dependent bile acid transporter (ASBT) retrieves bile acids from the small intestine and plays a pivotal role in enterohepatic circulation. Currently, high-resolution structures are available for two bacterial ASBT homologs (ASBTNM from Neisseria meningitides and ASBTYf from Yersinia frederiksenii), from which an elevator-style alternating-access mechanism has been proposed for substrate transport. A key concept in this model is that the substrate binds to the central cavity of the transporter so that the elevator-like motion can expose the bound substrate alternatingly to either side of the membrane during a transport cycle. However, no structure of an ASBT has been solved with a substrate bound in its central cavity, so how a substrate binds to ASBT remains to be defined. In this study, molecular docking, structure determination and functional analysis were combined to define and validate the details of substrate binding in ASBTYf. The findings provide coherent evidence to provide a clearer picture of how the substrate binds in the central cavity of ASBTYf that fits the alternating-access model.

Beschreibung: Sinorhizobium meliloti 1021 is a Gram-negative alphaproteobacterium with a robust capacity for carbohydrate metabolism. The enzymes that facilitate these reactions assist in the survival of the bacterium across a range of environmental niches, and they may also be suitable for use in industrial processes. SmoS is a dehydrogenase that catalyzes the oxidation of the commonly occurring sugar alcohols sorbitol and galactitol to fructose and tagatose, respectively, using NAD+ as a cofactor. The main objective of this study was to evaluate SmoS using biochemical techniques. The nucleotide sequence was codon-optimized for heterologous expression in Escherichia coli BL21 (DE3) Gold cells and the protein was subsequently overexpressed and purified. Size-exclusion chromatography and X-ray diffraction experiments suggest that SmoS is a tetramer. SmoS was crystallized, and crystals obtained in the absence of substrate diffracted to 2.1 Å resolution and those of a complex with sorbitol diffracted to 2.0 Å resolution. SmoS was characterized kinetically and shown to have a preference for sorbitol despite having a higher affinity for galactitol. Computational ligand-docking experiments suggest that tagatose binds the protein in a more energetically favourable complex than fructose, which is retained in the active site over a longer time frame following oxidation and reduces the rate of the reaction. These results supplement the inventory of biomolecules with potential for industrial applications and enhance the understanding of metabolism in the model organism S. meliloti.