Image-plate Data Research Articles

Refining instrument response functions with 3-D Monte Carlo simulations of differential hard x-ray spectrometers

Abstract Three x-ray spectrometers – the hard x-ray detector (HXRD), the bremsstrahlung MeV x-ray spectrometer (BMXS), and the hard x-ray image plate (HXIP) – areused to estimate hot-electron bremsstrahlung spectrum parameters for inertial confinement fusion experiments on OMEGA. Using 1-D deterministically calculated response functions, they show significantly different estimates of spectrum slope temperature. For all three detectors, 3-D Geant4 Monte Carlo simulations are developed and used to compute instrument response functions. Simulations explain features in raw image-plate data, but only significantly improve systematic errors in predicted detector channel signals for BMXS and do not entirely eliminate the discrepancy between estimates of slope temperature.

Redetermination of bis(acetylacetonato-κ2O,O′)(1,10-phenanthroline-κ2N,N′)manganese(II)

In the crystal structure of the title compound, [Mn(C5H7O2)2(C12H8N2)], the Mn2+ cation is coordinated by one bidentate 1,10-phenanthroline ligand and two acetyl­acetonate anions within a slightly distorted N2O4 octa­hedron. The asymmetric unit consists of one Mn2+ cation situated on a twofold rotation axis, one half of a 1,10-phenanthroline ligand and one acetyl­acetonate anion. In comparison with the previous determination based on visually estimated intensities recorded on precession photographs, the current redetermination with image-plate data reveals bond lengths and angles with much higher precision.

Refinement of Crystal Structure of a Magnetoelectric U-Type Hexaferrite Sr4Co2Fe36O60

Hexaferrites have long been used in technological applications such as permanent magnets and microwave applications because they retain their ferromagnetic and insulating properties up to temperatures much higher than room temperature. It is known that there are six main types of hexaferrites: M-type (Ba,Sr)Fe12O19, Y-type (Ba,Sr)2M2Fe12O22, W-type (Ba,Sr)M2Fe16O27, X-type (Ba,Sr)2M2Fe28O46, Z-type (Ba,Sr)3M2Fe24O41, and U-type (Ba,Sr)4M2Fe36O60, where M denotes a divalent metal ion. The crystal structures of these hexaferrites can be distinguished by stacking sequences of three basic blocks: S (spinel block), R [(Ba,Sr)Fe6O11] 2 , and T (Ba,Sr)2Fe8O14 (see the left panels of Fig. 1). After the discovery of a magnetoelectric (ME) effect in Y-type Ba0:5Sr1:5Zn2Fe12O22 showing a spin spiral magnetic order, hexaferrites have been attracting renewed attention as a new class of ME multiferroics which operate by applying low magnetic fields at high temperatures. Recently, a U-type hexaferrite, Sr4Co2Fe36O60, has been found to exhibit a low-field ME effect at room temperature. It is known that the U-type structure with the space group R 3m can be described as the sequence (RSR S TS )3, where the ( ) symbol means that the corresponding block turns 180 about the hexagonal c-axis. However, no literature which reports on its detailed crystal structure is available to date. Thus, to determine the detailed crystal structure of the U-type hexaferrite, we grew single crystals of the ME U-type hexaferrite Sr4Co2Fe36O60 and performed a single-crystal x-ray structure analysis. Single crystals of a U-type hexaferrite were grown by the Na2O–Fe2O3 flux method similar to that described in Refs. 8 and 16. We crushed one of the crystals into small pieces, and used one of the pieces (50 50 50 m) for the present single-crystal x-ray crystal structure analysis. To obtain the data for the crystal structure analysis, synchrotron diffraction measurements were performed at BL-8B of the Photon Factory, KEK. Oscillation photographs using an 18 keV x-ray were captured at room temperature by an imaging plate (IP) Weissenberg camera. For the image data processing of digital IP data and structure refinements, the programs RAPID and Crystal Structure (Rigaku) were used. We constructed a starting structural model of a U-type hexaferrite (RSR S TS stacking) by using known atomic coordinates of R, S, and T blocks in a Z-type hexaferrite (RSTSR S T S stacking) (Ref. 17). For the refinement, we regarded Co (atomic number = 27) as Fe (1⁄4 26) because their atomic form factors are practically indistinguishable. The obtained crystal data, the experimental condition, and the structural parameters are listed in Table I. The atomic coordinates in a unit cell and the thermal parameters are also listed in Table II. The atomic displacement parameters B of Fe(10) and O(1) sites are relatively large. In the case of Fe(10) site which is located at the center of a trigonal bipyramid sublattice, its anisotropic atomic displacement parameters remarkably extend along the c-axis (see Ref. 18). This implies that Fe(10) splits along this direction. A similar behavior of anisotropic atomic displacement parameters is reported for the Fe site in a trigonal bipyramid sublattice of an M-type hexaferrite BaFe12O19 (Ref. 19). In the case of the O(1) site, the large B is attributable to the nearest neighbor Sr(2) site which also has relatively large B. Based on the obtained structural data, we calculated valences of the respective Fe sites by using the bond valence sum (BVS) method. The obtained valences of the respective Fe sites are shown in Table II. As a result, the valences of six Fe sites: Me(1), Me(3), Me(4), Me(5), Me(7), and Me(13) are a b c S block

Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315

The phenylacetic acid (PAA) degradation pathway is the sole aerobic route for phenylacetic acid metabolism in bacteria and facilitates degradation of environmental pollutants such as styrene and ethylbenzene. The PAA pathway also is implicated in promoting Burkholderia cenocepacia infections in cystic fibrosis patients. Intriguingly, the first enzyme in the PAA pathway is present in two copies (paaK1 and paaK2), yet each subsequent enzyme is present in only a single copy. Furthermore, sequence divergence indicates that PaaK1 and PaaK2 form a unique subgroup within the adenylate-forming enzyme (AFE) superfamily. To establish a biochemical rationale for the existence of the PaaK paralogs in B. cenocepacia, we present high resolution x-ray crystal structures of a selenomethionine derivative of PaaK1 in complex with ATP and adenylated phenylacetate intermediate complexes of PaaK1 and PaaK2 in distinct conformations. Structural analysis reveals a novel N-terminal microdomain that may serve to recruit subsequent PAA enzymes, whereas a bifunctional role is proposed for the P-loop in stabilizing the C-terminal domain in conformation 2. The potential for different kinetic profiles was suggested by a structurally divergent extension of the aryl substrate pocket in PaaK1 relative to PaaK2. Functional characterization confirmed this prediction, with PaaK1 possessing a lower K(m) for phenylacetic acid and better able to accommodate 3' and 4' substitutions on the phenyl ring. Collectively, these results offer detailed insight into the reaction mechanism of a novel subgroup of the AFE superfamily and provide a clear biochemical rationale for the presence of paralogous copies of PaaK of B. cenocepacia.

Macromolecular powder diffraction: Structure solution via molecular replacement

Macromolecular powder diffraction is a burgeoning technique for protein structure solution - ideally suited for cases where no suitable single crystals are available. Over the past seven years, pioneering work by Von Dreele et al. [1,2] and Margiolaki et al. [3,4] has demonstrated the viability of this approach for several protein structures. Among these initial powder studies, molecular replacement solutions of insulin and turkey lysozyme into alternate space groups were accomplished. Pressing the technique further, Margiolaki et al. [5] executed the first molecular replacement of an unknown protein structure: the SH3 domain of ponsin, using data from a multianalyzer diffractometer. To demonstrate that cross-species molecular replacement using image plate data is also possible, we present the solution of hen egg white lysozyme using the 60% identical human lysozyme (PDB code: 1LZ1) as the search model. Due to the high incidence of overlaps in powder patterns, especially in more complex structures, we have used extracted intensities from five data sets taken at different salt concentrations in a multi-pattern Pawley refinement. The use of image plates severely increases the overlap problem due to lower detector resolution, but radiation damage effects are minimized with shorter exposure times and the fact that the entiremore » pattern is obtained in a single exposure. This image plate solution establishes the robustness of powder molecular replacement resulting from different data collection techniques.« less

Getting the most from image-plate data

Getting the most from image-plate data

Application of molecular replacement to protein powder data from image plates

Macromolecular structures can be solved via molecular replacement from powder diffraction data collected not only on multi-analyzer diffractometers but also on image plates. Diffraction peaks recorded on image plates are generally broader than those collected using an array of crystal analyzer detectors, but the image-plate data often allow the use of powder data to lower d-spacings. Owing to the high incidence of overlaps in powder patterns, which is especially evident for larger structures, a multi-pattern Pawley refinement is necessary in order to distinguish intensity peaks. This work utilized various salt concentrations to produce small lattice distortions, which resulted in shifts of Bragg peak positions, in a suite of five powder patterns. Using reflection structure factors obtained from this combined refinement, the structure of hen egg-white lysozyme was determined by molecular replacement using the 60% identical human lysozyme (PDB code 1lz1) as the search model. This work also expands upon previous work by presenting a full-scale multi-species analysis combined with an investigation of the sensitivity with regard to discrimination between incorrect fold types. To test the limits of this technique, extension to higher molecular-weight structures is ongoing.

Use of imaging plates at near saturation for high energy density particles

Since an imaging plate (IP) is sensitive to electron, ion, and x rays, it can be used as a detector for laser plasma experiment using ultraintense laser. Moreover, an IP has the advantageous features such as high sensitivity, wide dynamic range, and high spatial resolution. Even though IP itself has a considerable wide dynamic range up to 10(5), the IP data have appeared often saturated at an IP reading device. We propose a reading technique by inserting optical density filters so that an apparently saturated IP data can be saved.

In situ study of icosahedral Zn–Mg–Dy and Co-rich decagonal Al–Co–Ni at high pressuresand high temperatures

An in situ high-pressure high-temperature x-ray diffraction study on single-crystallineicosahedral Zn–Mg–Dy up to 12.5(4) GPa at 873 K and powdered Co-rich decagonalAl–Co–Ni up to 12.3(4) GPa at 973 K has been performed using a heatable diamond-anvilcell and synchrotron radiation. Quantitative reciprocal-space reconstruction from imageplate data was used for evaluating the single-crystal data. The compressibility of thematerials at ambient temperature was determined from x-ray powder diffraction up to30.3(2) GPa for icosahedral Zn–Mg–Dy and 61.4(1) GPa for Co-rich decagonalAl–Co–Ni. The bulk modulus at zero pressure and its pressure derivative weredetermined from fitting third-order Birch–Murnaghan equations of state asK0 = 92(4) GPa,K′ = 3.1(3) for icosahedralZn–Mg–Dy and K0 = 120(11) GPa, K′ = 7.1(7) for Co-rich decagonal Al–Co–Ni, respectively. The compressibilities of the quasicrystals arediscussed with respect to their structure types and the available literature data. To afirst approximation, a linear dependency of the squared electron density at theborder of the Wigner–Seitz atomic cell from the ratio of the bulk modulus and themolar volume was found. This behaviour is comparable to that of periodic alloys.

Redetermination ofcatena-poly[[[bis(ethylenediamine)platinum(II)]-μ-chloro-[bis(ethylenediamine)platinum(IV)]-μ-chloro] tetrakis(hexafluorophosphate)

The structure of the title compound, {[PtII/IVCl(C2H8N2)2](PF6)2}n or [PtII(C2H8N2)2][PtIVCl2(C2H8N2)2](PF6)4, has been redetermined [Matsushita (1993). Synth. Met. 56, 3401–3406] from image-plate data. No superstructure was observed, in contrast to the situation in related compounds. The linear chain structure consists of square-planar [Pt(en)2]2+ and elongated octa­hedral trans-[PtCl2(en)2]2+ cations (en is ethyl­enediamine) stacked alternately, bridged by the Cl atoms, along the b axis. The Pt atom is located on an inversion centre and the Cl atom (site symmetry 2) is disordered over two sites, resulting in PtIV–Cl and PtII⋯Cl bond distances of 2.327 (4) and 3.191 (4) Å, respectively. The δ structural parameter, indicating the mixed-valence state of the Pt atoms, is 0.729.

A single-crystal high-pressure x-ray diffraction study of decagonal Al–Co–Cu up to 19.1GPa

An in situ single-crystal high-pressure x-ray diffraction study of decagonal Al–Co–Cu up to19.1 GPa has been performed using diamond anvil cells and synchrotron radiation.Quantitative reciprocal space reconstruction from image plate data was used fordata analysis. No significant variations with pressure were observed in Braggas well as diffuse scattering, indicating the high stability of the quasiperiodicstructure in the investigated pressure range. The bulk modulus at zero pressure wasdetermined from fitting a second-order Birch–Murnaghan equation of state asK0 = 131(8) GPa. The influence of different crystal orientations on the accessible amount of reciprocalspace data is discussed.

Crystal structure of a tandem cystathionine‐β‐synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 Å resolution

Crystal structure of a tandem cystathionine‐β‐synthase (CBS) domain protein (TM0935) from <i>Thermotoga maritima</i> at 1.87 Å resolution

Peculiarity and defect structure of the natural and synthetic zeolite mordenite: A single-crystal X-ray study

Single-crystal X-ray data were collected from a natural fibrous mordenite crystal of composition K2.99Ca1.85Na1.06Al7.89Si40.15O96⋅28H2O and from a platy synthetic mordenite crystal of composition Na6Al6.02Si42.02O96⋅19H2O. Diffraction data were measured with a point detector using a sealed X-ray tube and an image plate using synchrotron radiation, respectively. Both structures exhibit the same defect features visible in difference-Fourier maps. Domains of the entire Cmcm framework structure are reproduced by a non-crystallographic (001) mirror plane at z = 0 and z = 1/2. An identical description is a shift of framework domains 1/2 along the c axis. The concentration of this defect domain is 2.7(2) and 3.1(1)% for the natural and synthetic mordenite crystals, respectively. Reproductions of reciprocal layers from synchrotron image-plate data reveal diffuse scattering for hkl layers with l = 2n + 1. The diffuseness of these layers is not homogeneous but concentrates in the form of halos around selected reflections allowed for C-centering. Diffuse features in electron diffraction patterns of natural and synthetic mordenite have been described before and were interpreted either as evidence of c/2 faults or intergrowth with different mordenite-related structure-types. We have modeled a (100) defect layer that is modified from the mordenite characteristic puckered sheet of six-membered rings and allows coherent intergrowth of identical structural subunits shifted by c/2. These defect domains do not influence or obstruct the 12-membered ring-channels characteristic of this zeolite. The major difference in Si,Al distribution between the two samples is that the natural crystal has Al strongly enriched at T3, which is part of the four-membered rings. We suggest that a synergetic effect between extraframework cations and Si, Al ordering during crystal growth is responsible for Al enrichment in natural mordenite with ca. 2 Ca p.f.u. close to T3.

Resonant X-ray diffraction using high-resolution image-plate data

The experimental setup for the collection of synchrotron X-ray powder diffraction data from samples with high absorption (μR&gt; 10) is described. It consists of a combination of a vacuum chamber with an image-plate system. A numerical absorption correction for the applied geometry has been derived and the data were corrected accordingly. Values forf ′(Er) andf ′′(Er) were refined from eight measurements on Er5Re2O12above and below the ErLIIIabsorption edge. Successful refinement of the crystallographic data has verified the high quality of the collected intensities.

Electron density study of KNiF3 by the vacuum-camera-imaging plate method.

The electron density measurements of KNiF(3), nickel potassium trifluoride, by the vacuum-camera-imaging plate (VCIP) method and using a four-circle diffractometer with scintillation counter, are performed and compared. In the IP (imaging plate) case evacuation allowed the background around peaks to be reduced 50 times, which significantly increased the accuracy of the data, especially for high-angle reflections. A new VIIPP program for visualizing and integration of IP data was designed to treat the data, in which the correction for oblique incidence was applied. The resulting electron density reproduces all the features of the accurate conventional measurement.

1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints.

The X-ray structure of the T39K mutant of the variable domain of a human immunoglobulin kappa light chain has been determined at room temperature to 1.7 A resolution with a conventional R factor of 0. 182. T39K crystallizes in the triclinic space group P1 [a = 35.4 (1), b = 40.1 (1), c = 43.1 (1) A, alpha = 66.9 (1), beta = 85.4 (1), gamma = 73.8 (1) degrees ]. The unit-cell contains two monomers, related by a non-crystallographic twofold axis. The use of a novel type of local non-crystallographic symmetry restraints on related isotropic displacement parameters and 1-4 distances as incorporated in the refinement program SHELXL improves the model and quality of the maps, but local differences between both monomers in areas subject to different packing contacts can still be observed. 12 overall anisotropic scaling parameters were refined. These may have compensated for the difficulties in accurately scaling single rotation axis image plate data from a triclinic crystal, because of the scarcity of common equivalent reflections. The final model has been used to perform a number of tests on anisotropic scaling, non-crystallographic symmetry, anisotropic refinement, determination of standard uncertainties and bulk solvent correction. It is remarkable that removal of the NCS restraints from the final model caused Rfree to increase. These tests clarify the strategies for optimum use of SHELXL for refinement at medium as opposed to atomic resolution.

Preparation and Crystal Structure of Cr4(Si2O7)X2(X= Cl, Br): The First Chromous Halide-Disilicates

The new chromous oxo-halides Cr4(Si2O7)X2(X= Cl, Br) which adopt a hitherto unknown structure type were obtained as small, deep blue crystals from mixtures of Cr2O3, Cr, SiO2, and CrCl3or CrBr2, respectively, in sealed silica tubes at elevated temperatures (Cr4(Si2O7)Cl2: 1000°C; Cr4(Si2O7)Br2: 1220°C) in the presence of a mineralizer (NH4Cl; excess of CrBr2). They show remarkable stability against oxidation. The crystal structures of both Cr4(Si2O7)Cl2(Cr4(Si2O7)Br2) have been determined and refined from X-ray single crystal data (PcNo. 7),Z= 4,a= 6.3853(7) Å (6.414(3) Å),b= 12.707(2) Å (12.829(6) Å),c= 10.448(1) Å (10.540(6) Å), β = 92.37(1)° (91.61(4)°)). Four circle diffractometer data were used for the refinement of the chloride structure while imaging plate data were used for the bromide (conventional residualR1 = 0.016 (0.053) for 4761 (3491) Fo > 4σ, 4945 (3911) independent reflections, 273 (273) parameters). The structure consists of eight crystallographically different Cr2+with c.n. five or six and mixed coordination by oxygen and halogen. All coordination polyhedra are highly distorted as a result of the Jahn–Teller effect. Two independent disilicate groups exhibit almost eclipsed conformation with bridging angles (Si–O–Si) of 145.8° and 138.4° for the chloride and 146.3° and 140.8° for the bromide.

A comparison of serial and imaging-plate data collection: the low-temperature charge density ofDL-histidine

A comparison of serial and imaging-plate data collection: the low-temperature charge density of<scp>DL</scp>-histidine

Synthesis of a novel open-framework sulfide, CuGe2S5.(C2H5)4N, and its structure solution using synchrotron imaging plate data

Synthesis of a novel open-framework sulfide, CuGe2S5.(C2H5)4N, and its structure solution using synchrotron imaging plate data

Weissenberg camera for macromolecules with imaging plate data collection system at the Photon Factory: Present status and future plan (invited)

A Weissenberg camera for macromolecules with imaging plate data collection system at BL6A and BL18B stations in the Photon Factory is introduced and evaluated. The special feature of these systems is considered matching for both SR-x rays and protein crystallography. This system is user-friendly and can collect a large amount of data to higher resolution from the crystal with large unit cell dimensions. A newly developed camera can be used as a time-resolved Laue camera and a Weissenberg camera. A large image reader (IPR4080) that can scan 400×400 mm2 and 400×800 mm2 sizes of imaging plates has been developed and evaluated. The new data collection system combined with the new camera and IPR4080 will be installed at the BL18B station in October 1994.