Crystalline transfer RNA: the three-dimensional Patterson function at 12-angstrom resolution

An orthorhombic form of crystalline formylmethionine transter RNA has been obtained which contains one molecule as the asymmetric unit of the unit cell. Three-dimensional x-ray diffraction data have been collected up to a resolution of 12 angstroms, and from this a Patterson function has been calculated. The function contains an elongated ridge of interatomic vectors parallel to the c-axis of the crystal. Analysis of the function suggests that the molecules are elogated and dimerized in an overlapping antiparrael fashion along the c-axis. The dimer has a length near 109 angstroms and a width of 35 angstroms in one direction. The individual molecular length is approximately 80 angstroms with an irregular cross section measuring 25 by 35 angstrms.     

Single crystals of transfer RNA: an x-ray diffraction study

Large single crystals of formylmethionyl transfer RNA have been prepared. An x-ray diffraction study shows that the material crystallizes in a hexagonal lattice with a equal to 170 angstroms, c equal to 234 angstroms. The diffraction pattern extends to spacings just under 20 angstroms at present. The crystals are heavily hydrated, containing 88 percent water.     

Natural NaAlSi(3)O(8)-hollandite in the shocked sixiangkou meteorite

The hollandite high-pressure polymorph of plagioclase has been identified in shock-induced melt veins of the Sixiangkou L6 chondrite. It is intimately intergrown with feldspathic glass within grains previously thought to be "maskelynite." The crystallographic nature of the mineral was established by laser micro-Raman spectroscopy and x-ray diffraction. The mineral is tetragonal with the unit cell parameters a = 9.263 +/- 0.003 angstroms and c = 2.706 +/- 0.003 angstroms. Its occurrence with the liquidus pair majorite-pyrope solid solution plus magnesiowustite sets constraints on the peak pressures that prevailed in the shock-induced melt veins. The absence of a calcium ferrite-structured phase sets an upper bound for the crystallization of the hollandite polymorph near 23 gigapascals.     

Flash X-ray Microscopy

Soft x-ray contact microscopy, utilizing single-shot exposures of approximately 60 nanoseconds duration in polymethyl methacrylate, has been realized with a resolution of 300 angstroms. The radiation spectrum is intense in the "window" between 23 and 44 angstroms where water is transparent compared to biological materials, and therefore permits viewing of wet samples.     

Structure of recombinant human renin, a target for cardiovascular-active drugs, at 2.5 A resolution

The x-ray crystal structure of recombinant human renin has been determined. Molecular dynamics techniques that included crystallographic data as a restraint were used to improve an initial model based on porcine pepsinogen. The present agreement factor for data from 8.0 to 2.5 angstroms (A) is 0.236. Some of the surface loops are poorly determined, and these disordered regions border a 30 A wide solvent channel. Comparison of renin with other aspartyl proteinases shows that, although the structural cores and active sites are highly conserved, surface residues, some of which are critical for specificity, vary greatly (up to 10A). Knowledge of the actual structure, as opposed to the use of models based on related enzymes, should facilitate the design of renin inhibitors.     

Structure of langmuir-blodgett films of disk-shaped molecules determined by atomic force microscopy

Monolayer Langmuir-Blodgett films of a discotic mesogen have been studied with atomic force microscopy (AFM). These measurements confirm the "edge on" arrangement for the disk-shaped molecules suggested by surface pressure-area isotherms and show that the molecules form columns that are separated by 17.7 angstroms +/- 10 percent. Column alignment is found to be predominantly along the film deposition direction, with an angular spread of 35 degrees . The AFM images also show that the mean disk separation within the columns is 5.1 +/- 1.3 angstroms, in good agreement with x-ray diffraction (XRD) results. Roomtemperature XRD measurements on bulk samples of the same material indicate a disordered-hexagonal liquid crystalline mesophase, with a column-to-column spacing of 19.9 +/- 0.2 angstroms.     

Imidodiphosphate and pyrophosphate: possible biological significance of similar structures

The structure of sodium imidodiphosphate has been determined by single crystal x-ray diffraction. The P-N-P bond angle (127.2 degrees) and P-N bond distance (1.68 angstroms) are remarkably similar to newly refined values for the P-O-P bond angle (128.6 degrees) and the bridging P-O bond distance (1.63 angstroms) of sodium pyrophosphate. This close similarity may explain why P-N-P linkages in algal "polyphosphates" escaped detection until recently and why adenosine triphosphate analogs with this linkage mimic adenosine triphosphate so closely.     

The Framework Topology of ZSM-18, a Novel Zeolite Containing Rings of Three (Si,Al)-O Species

ZSM-18 is the first known aluminosilicate zeolite to contain rings of three (Si,Al)-O species (3-rings). Its framework topology has been determined by hypothetical model building, subsequent constrained distance and angle least-squares refinements of atomic coordinates, and x-ray powder diffraction pattern simulations. Its channel structure is characterized by a linear unidimensional 12-ring channel, with an approximate pore opening of 7.0 angstroms. In addition, the channels are lined with pockets that are capped by 7-rings with dimensions of 2.8 angstroms by 3.5 angstroms. An intraframework packing model of the organic moiety used in the synthesis suggests that a strong templating effect may be responsible for the formation of this unusual zeolite structure.     

Gas adsorption sites in a large-pore metal-organic framework

The primary adsorption sites for Ar and N2 within metal-organic framework-5, a cubic structure composed of Zn4O(CO2)6 units and phenylene links defining large pores 12 and 15 angstroms in diameter, have been identified by single-crystal x-ray diffraction. Refinement of data collected between 293 and 30 kelvin revealed a total of eight symmetry-independent adsorption sites. Five of these are sites on the zinc oxide unit and the organic link; the remaining three sites form a second layer in the pores. The structural integrity and high symmetry of the framework are retained throughout, with negligible changes resulting from gas adsorption.     

Neutron diffraction of cell membranes (myelin)

Small-angle neutron diffraction (wavelength 4.05 angstroms) of human and rabbit sciatic nerve has been carried out by means of the Brookhaven high flux beam reactor with an automated slit camera. Most of the free water of the nerves was substituted in order to minimize incoherent scatter of hydrogen atoms. The differences in amplitude and phase shifts between neutrons and x-rays resulted in a neutron diffraction pattern that was completely different from the x-ray pattern. The neutron pattern consisted of a single peak of about 89-angstrom spacing in the region examined (up to 6-angstrom spacing). The strong third, fourth, and fifth order reflections (about 60, 45, and 36 angstroms) seen in the x-ray pattern were suppressed. The neutron data indicated a strong scattering from one portion of the membrane.     

The structure of ferrihydrite, a nanocrystalline material

Despite the ubiquity of ferrihydrite in natural sediments and its importance as an industrial sorbent, the nanocrystallinity of this iron oxyhydroxide has hampered accurate structure determination by traditional methods that rely on long-range order. We uncovered the atomic arrangement by real-space modeling of the pair distribution function (PDF) derived from direct Fourier transformation of the total x-ray scattering. The PDF for ferrihydrite synthesized with the use of different routes is consistent with a single phase (hexagonal space group P6(3)mc; a = approximately 5.95 angstroms, c = approximately 9.06 angstroms). In its ideal form, this structure contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis delta-Keggin cluster. Real-space fitting indicates structural relaxation with decreasing particle size and also suggests that second-order effects such as internal strain, stacking faults, and particle shape contribute to the PDFs.     

Antiprismatic Coordination about Xenon: The Structure of Nitrosonium Octafluoroxenate(VI)

The structure of nitrosonium octafluoroxenate(VI), 2NOF . XeF(6), has been determined by means of single-crystal x-ray counter methods (R-index = 0.046, weighted R-index = 0.042). The space group is Pnma, with a = 8.914(10) angstroms, b = 5.945(10) angstroms, and c = 12.83(2) angstroms (the numbers in parentheses are the standard deviations to the least significant digit or digits); the calculated density (rho) is 3.354 grams per cubic centimeter, and there are four formula units per unit cell. The material consists of well-separated NO(+) and (XeF(8))(2-) ions; the structural formula is thus (NO)(2) (XeF(8)). The anion configuration is that of a slightly distorted Archimedean antiprism. The observed distortion appears incompatible with a lone-pair repulsion model. Xenon-fluorine bond lengths of 1.971(7), 1.946(5), 1.958(7), 2.052(5), and 2.099(5) angstroms were found.     

Precision Lattice-Parameter Determination of (Mg,Fe)SiO3 Tetragonal Garnets

The tetragonal garnet (Mg,Fe)SiO(3) is a high-pressure phase of pyroxene that is thought to be a major constituent of the earth's upper mantle. Its crystal structure is similar to that of cubic garnet, but it is slightly distorted to tetragonal symmetry so that its x-ray powder diffraction pattern shows a very small line splitting. A suite of tetragonal garnets with different compositions in the MgSiO(3)-rich portion of the MgSiO(3)-FeSiO(3) system was synthesized at about 20 gigapascals and 2000 degrees C. The lattice parameters a and c of quenched samples were determined by whole-powder-pattern decomposition analysis of Fe Kalpha x-ray powder diffraction data, which has the capacity to resolve to a high degree heavily overlapping reflections. It was found that the lattice parameters can be obtained from the following equations; a (in angstroms) = 11.516 + 0.088x and c (in angstroms) = 11.428 + 0.157x, where x, teh mole fraction of FeSiO(3), is 0.0 相似文献   

Structures from anomalous diffraction of native biological macromolecules

Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.     

Crystal Structure of the Solid Electrolyte, RbAg4I5

The crystal structure of the solid electrolyte RbAg(4)I(5) has been determined from single-crystal x-ray diffraction counter data. There are four RbAg(4)I(5) in a cubic unit cell with a = 11.24 A. The structure refinement, by least squares, is based on space group P4(1)3 (O(7)). The arrangement of the iodide ions is similar to that of the manganese atoms in beta-manganese, and provides 56 iodide tetrahedra per unit cell, which share faces in such manner as to provide diffusion paths for the silver ions. The occurrence of the two low-temperature phases of RbAg(4)I(5) has been established by x-ray diffraction and optical examination.     

A Synchrotron X-ray Study of a Solid-Solid Phase Transition in a Two-Dimensional Crystal

A measurement and interpretation on a molecular level of a phase transition in an ordered Langmuir monolayer is reported. The diagram of surface pressure (pi) versus molecular area of a monolayer of chiral (S)-[CF(3)-(CF(2))(9)-(CH(2))(2)-OCO-CH(2)-CH (NH(3)(+))CO(2)(-)] over water shows a change in slope at about pi(s)= 25 millinewtons per meter. Grazing-incidence x-ray diffraction and specular reflectivity measurements indicate a solid-solid phase transition at pi(s). The diffraction pattren at low pressures reveals two diffraction peaks of equal intensities, with lattice spacings d of 5.11 and 5.00 angstroms; these coalesce for pi >/=pi(s). Structural models that fit the diffraction data show that at pi> pi(s) the molecules pack in a two-dimensional crystal with the molecules aligned vertically. At pi < pi(s) there is a molecular tilt of 16 degrees +/- 7 degrees . Independent x-ray reflectivity data yield a tilt of 26 degrees +/- 7 degrees . Concomitant with the tilt, the diffraction data indicate a transition from a hexagonal to a distorted-hexagonal lattice. The hexagonal arrangement is favored because the -(CF(2))(9)CF(3) moiety adopts a helical conformation. Compression to 70 millinewtons per meter yields a unit cell with increased crystallinity and a coherence length exceeding 1000 angstroms.     

X-ray holograms at improved resolution: a study of zymogen granules

X-ray holography offers the possibility of three-dimensional microscopy with resolution higher than that of the light microscope and with contrast based on x-ray edges. In principle, the method is especially advantageous for biological samples if x-rays in the wavelength region between the carbon and oxygen K edges are used. However, until now the achieved resolution has not exceeded that of the light microscope because of the poor coherence properties of the x-ray sources and the low resolution of the detectors that were available. With a recently developed x-ray source based on an undulator on an electron storage ring, and high resolution x-ray resist, a hologram has been recorded at about 400-angstrom resolution. The experiment utilized x-rays with wavelengths of 24.7 angstroms and required a 1-hour exposure of the pancreatic zymogen granules under study.     

Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A

The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer.     

Colossal Magnetoresistance Without Mn3+/Mn4+ Double Exchange in the Stoichiometric Pyrochlore Tl2Mn2O7

Structural analysis from powder neutron and single-crystal x-ray diffraction data for a sample of the Tl2Mn2O7 pyrochlore, which exhibits colossal magnetoresistance (CMR), shows no deviations from ideal stoichiometry. This analysis gives an Mn-O distance of 1.90 angstroms, which is significantly shorter than the Mn-O distances (1.94 to 2.00 angstroms) observed in phases based on LaMnO3 perovskites that exhibit CMR. Both results in Tl2Mn2O7 indicate oxidation states very close to Tl23+Mn24+O7. Thus, Tl2Mn2O7 has neither mixed valence for a double-exchange magnetic interaction nor a Jahn-Teller cation such as Mn3+, both of which were thought to have an important function in CMR materials. An alternate mechanism for CMR in Tl2Mn2O7 based on magnetic ordering driven by superexchange and strong spin-fluctuation scattering above the Curie temperature is proposed here.     

Structural studies on transfer RNA: preliminary crystallographic analysis

Single-crystal diffraction patterns from Escherichia coli leucine tRNA and yeast formylmethionine tRNA show a tetragonal lattice for the former, with a = 46 angstroms and c = 137 angstroms, and a hexagonal lattice for the latter, with a = 115 angstroms and c = 137 angstroms. Initial analysis suggests a molecule with a long, double helix parallel to the c-axis for both crystals.