scholarly journals Supplemental Material: Syncing fault rock clocks: Direct comparison of U-Pb carbonate and K-Ar illite fault dating methods

2020 ◽  
Author(s):  
Catherine Mottram ◽  
et al.
Keyword(s):  
Structural Data ◽  
X Ray Diffraction ◽  
Fault Rock ◽  
Data Set ◽  
X Ray ◽  
Dating Methods ◽  
Carbonate Sample

Full analytical materials, gouge and detailed carbonate sample descriptions and locations, summary of additional U-Pb geochronology plots and interpretation, structural data, and Data Set S1 (K-Ar results), Data Set S2 (X-ray diffraction results), Data Set S3 (U-Pb carbonate results), and Data Set S4 (U-Pb standard reproducibility). <br>

scholarly journals Supplemental Material: Syncing fault rock clocks: Direct comparison of U-Pb carbonate and K-Ar illite fault dating methods

2020 ◽  
Author(s):  
Catherine Mottram ◽  
et al.
Keyword(s):  
Structural Data ◽  
X Ray Diffraction ◽  
Fault Rock ◽  
Data Set ◽  
X Ray ◽  
Dating Methods ◽  
Carbonate Sample

Full analytical materials, gouge and detailed carbonate sample descriptions and locations, summary of additional U-Pb geochronology plots and interpretation, structural data, and Data Set S1 (K-Ar results), Data Set S2 (X-ray diffraction results), Data Set S3 (U-Pb carbonate results), and Data Set S4 (U-Pb standard reproducibility). <br>

Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?

2009 ◽  
Vol 16 (2) ◽  
pp. 191-204 ◽  
Author(s):  
Sofia Macedo ◽  
Maria Pechlaner ◽  
Walther Schmid ◽  
Martin Weik ◽  
Katsuko Sato ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Active Sites ◽  
Structural Data ◽  
Potassium Hexacyanoferrate ◽  
X Ray Diffraction ◽  
Metal Centre ◽  
Data Set ◽  
Synchrotron Source ◽  
X Ray ◽  
X Ray Crystallography

One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV–Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV–Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.

Tubulin structure at intermediate resolution

1995 ◽  
Vol 53 ◽  
pp. 852-853
Author(s):  
K. H. Downing ◽  
S. G. Wolf ◽  
E. Nogales
Keyword(s):  
High Resolution ◽  
Structural Data ◽  
Therapeutic Drug ◽  
Zinc Ions ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Negative Stain ◽  
Functional Mechanisms ◽  
Tubulin Structure

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.

Compressibility of β-As4S4: an in situ high-pressure single-crystal X-ray study

2012 ◽  
Vol 76 (4) ◽  
pp. 963-973 ◽  
Author(s):  
G. O. Lepore ◽  
T. Boffa Ballaran ◽  
F. Nestola ◽  
L. Bindi ◽  
D. Pasqual ◽  
...  
Keyword(s):  
Pressure Range ◽  
Substantial Reduction ◽  
Structural Data ◽  
Unit Cell ◽  
Van Der Waals Interactions ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Intermolecular Distances

AbstractAmbient temperature X-ray diffraction data were collected at different pressures from two crystals of β-As4S4, which were made by heating realgar under vacuum at 295ºC for 24 h. These data were used to calculate the unit-cell parameters at pressures up to 6.86 GPa. Above 2.86 GPa, it was only possible to make an approximate measurement of the unit-cell parameters. As expected for a crystal structure that contains molecular units held together by weak van der Waals interactions, β-As4S4 has an exceptionally high compressibility. The compressibility data were fitted to a third-order Birch–Murnaghan equation of state with a resulting volume V0 = 808.2(2) Å3, bulk modulus K0 = 10.9(2) GPa and K' = 8.9(3). These values are extremely close to those reported for the low-temperature polymorph of As4S4, realgar, which contains the same As4S4 cage-molecule. Structural analysis showed that the unit-cell contraction is due mainly to the reduction in intermolecular distances, which causes a substantial reduction in the unit-cell volume (∼21% at 6.86 GPa). The cage-like As4S4 molecules are only slightly affected. No phase transitions occur in the pressure range investigated.Micro-Raman spectra, collected across the entire pressure range, show that the peaks associated with As–As stretching have the greatest pressure dependence; the S–As–S bending frequency and the As–S stretching have a much weaker dependence or no variation at all as the pressure increases; this is in excellent agreement with the structural data.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of a hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) fromCoffea canephorainvolved in chlorogenic acid biosynthesis

2012 ◽  
Vol 68 (7) ◽  
pp. 824-828 ◽  
Author(s):  
Laura A. Lallemand ◽  
James G. McCarthy ◽  
Sean McSweeney ◽  
Andrew A. McCarthy
Keyword(s):  
Structural Data ◽  
Coffea Canephora ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Key Enzyme ◽  
Substrate Specifities ◽  
Drop Technique ◽  
Better Than

Chlorogenic acids (CGAs) are a group of soluble phenolic compounds that are produced by a variety of plants, includingCoffea canephora(robusta coffee). The last step in CGA biosynthesis is generally catalysed by a specific hydroxycinnamoyl-CoA quinate hydroxycinnamoyltransferase (HQT), but it can also be catalysed by the more widely distributed hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT). Here, the cloning and overexpression of HCT fromC. canephorainEscherichia colias well as its purification and crystallization are presented. Crystals were obtained by the sitting-drop technique at 293 K and X-ray diffraction data were collected on the microfocus beamline ID23-2 at the ESRF. The HCT crystals diffracted to better than 3.0 Å resolution, belonged to space groupP42212 with unit-cell parametersa=b= 116.1,c= 158.9 Å and contained two molecules in the asymmetric unit. The structure was solved by molecular replacement and is currently under refinement. Such structural data are needed to decipher the molecular basis of the substrate specifities of this key enzyme, which belongs to the large plant acyl-CoA-dependent BAHD acyltransferase superfamily.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of the effector protein PevD1 fromVerticillium dahliae

2012 ◽  
Vol 68 (7) ◽  
pp. 802-805 ◽  
Author(s):  
Lei Han ◽  
Zheng Liu ◽  
Xinqi Liu ◽  
Dewen Qiu
Keyword(s):  
Pathogenic Fungus ◽  
Sodium Formate ◽  
Diffusion Method ◽  
Effector Protein ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Dispersion Method ◽  
Data Set ◽  
X Ray ◽  
Anomalous Signal

The effector protein PevD1 from the pathogenic fungusVerticillium dahliaewas purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals appeared in a solution consisting of 4.0 Msodium formate. A native data set was collected at 1.9 Å resolution at 100 K using an in-house X-ray source. Because of the absence of useful methinione in the protein sequence, derivative crystals that contained iodine were obtained by soaking in 1.25 Mpotassium iodide, and a data set that contained anomalous signal was collected using the same X-ray facility at a wavelength of 1.54 Å. The single-wavelength anomalous dispersion method was used to successfully solve the structure based on the anomalous signal generated from iodine.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of UspE fromEscherichia coli

2014 ◽  
Vol 70 (12) ◽  
pp. 1640-1642 ◽  
Author(s):  
Yongbin Xu ◽  
Chun-Shan Quan ◽  
Xuanzhen Jin ◽  
Xiaoling Jin ◽  
Jing Zhao ◽  
...  
Keyword(s):  
Stress Proteins ◽  
Gel Filtration ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
E Coli ◽  
Vapour Diffusion ◽  
Induced Genes

Universal stress proteins (Usps) are among the most highly induced genes when bacteria are subjected to several stress conditions such as heat shock, nutrient starvation or the presence of oxidants or other stress agents.Escherichia colihas five small Usps and one tandem-type Usp. UspE (or YdaA) is the tandem-type Usp and consists of two Usp domains arranged in tandem. To date, the structure of UspE remains to be elucidated. To contribute to the molecular understanding of the function of the tandem-type UspE, UspE fromE. coliwas overexpressed and the recombinant protein was purified using Ni–NTA affinity, Q anion-exchange and gel-filtration chromatography. Crystals of UspE were obtained by sitting-drop vapour diffusion. A diffraction data set was collected to a resolution of 3.2 Å from flash-cooled crystals. The crystals belonged to the tetragonal space groupI4122 orI4322, with unit-cell parametersa=b= 121.1,c = 241.7 Å.

scholarly journals X-Ray Single Crystal Structural Analysis of Magnetically Oriented Microcrystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C1138-C1138
Author(s):  
Chiaki Tsuboi ◽  
Kazuki Aburaya ◽  
Shingo Higuchi ◽  
Fumiko Kimura ◽  
Masataka Maeyama ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Single Crystal ◽  
Three Dimensional ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Data Set ◽  
Uv Curable ◽  
X Ray

We have developed magnetically oriented microcrystal array (MOMA) technique that enables single crystal X-ray diffraction analyses from microcrystalline powder. In this method, microcrystals suspended in a UV-curable monomer matrix are there-dimensionally aligned by special rotating magnetic field, followed by consolidation of the matrix by photopolymerization. From thus achieved MOMAs, we have been succeeded in crystal structure analysis for some substances [1, 2]. Though MOMA method is an effective technique, it has some problems as follows: in a MOMA, the alignment is deteriorated during the consolidation process. In addition, the sample microcrystals cannot be recovered from a MOMA. To overcome these problems, we performed an in-situ X-ray diffraction measurement using a three-dimensional magnetically oriented microcrystal suspension (3D MOMS) of L-alanine. An experimental setting of the in-situ X-ray measurement of MOMS is schematically shown in the figure. L-alanine microcrystal suspension was poured into a glass capillary and placed on the rotating unit equipped with a pair of neodymium magnets. Rotating X-ray chopper with 10°-slits was placed between the collimator and the suspension. By using this chopper, it was possible to expose the X-ray only when the rotating MOMS makes a specific direction with respect to the impinging X-ray. This has the same effect as the omega oscillation in conventional single crystal measurement. A total of 22 XRD images of 10° increments from 0° to 220° were obtained. The data set was processed by using conventional software to obtain three-dimensional molecular structure of L-alanine. The structure is in good agreement with that reported for the single crystal. R1 and wR2 were 6.53 and 17.4 %, respectively. RMSD value between the determined molecular structure and the reported one was 0.0045 Å. From this result, we conclude that this method can be effective and practical to be used widely for crystal structure analyses.

Sergevanite, Na15(Ca3Mn3)(Na2Fe)Zr3Si26O72(OH)3·H2O, a new eudialyte-group mineral from the Lovozero alkaline massif, Kola Peninsula

2020 ◽  
Vol 58 (4) ◽  
pp. 421-436 ◽  
Author(s):  
Nikita V. Chukanov ◽  
Sergey M. Aksenov ◽  
Igor V. Pekov ◽  
Dmitriy I. Belakovskiy ◽  
Svetlana A. Vozchikova ◽  
...  
Keyword(s):  
Kola Peninsula ◽  
Structural Data ◽  
New Mineral ◽  
X Ray Diffraction ◽  
Calculated Density ◽  
Eudialyte Group ◽  
Group Mineral ◽  
X Ray ◽  
Mohs Hardness ◽  
Alkaline Massif

ABSTRACT The new eudialyte-group mineral sergevanite, ideally Na15(Ca3Mn3)(Na2Fe)Zr3Si26O72(OH)3·H2O, was discovered in highly agpaitic foyaite from the Karnasurt Mountain, Lovozero alkaline massif, Kola Peninsula, Russia. The associated minerals are microcline, albite, nepheline, arfvedsonite, aegirine, lamprophyllite, fluorapatite, steenstrupine-(Ce), ilmenite, and sphalerite. Sergevanite forms yellow to orange-yellow anhedral grains up to 1.5 mm across and the outer zones of some grains of associated eudialyte. Its luster is vitreous, and the streak is white. No cleavage is observed. The Mohs' hardness is 5. Density measured by equilibration in heavy liquids is 2.90(1) g/cm3. Calculated density is equal to 2.906 g/cm3. Sergevanite is nonpleochroic, optically uniaxial, positive, with ω = 1.604(2) and ε = 1.607(2) (λ = 589 nm). The infrared spectrum is given. The chemical composition of sergevanite is (wt.%; electron microprobe, H2O determined by HCN analysis): Na2O 13.69, K2O 1.40, CaO 7.66, La2O3 0.90, Ce2O3 1.41, Pr2O3 0.33, Nd2O3 0.64, Sm2O3 0.14, MnO 4.15, FeO 1.34, TiO2 1.19, ZrO2 10.67, HfO2 0.29, Nb2O5 1.63, SiO2 49.61, SO3 0.77, Cl 0.23, H2O 4.22, –O=Cl –0.05, total 100.22. The empirical formula (based on 25.5 Si atoms pfu, in accordance with structural data) is H14.46Na13.64K0.92Ca4.22Ce0.27La0.17Nd0.12Pr0.06Sm0.02Mn1.81Fe2+0.58Ti0.46Zr2.67Hf0.04Nb0.38Si25.5S0.30Cl0.20O81.35. The crystal structure was determined using single-crystal X-ray diffraction data. The new mineral is trigonal, space group R3, with a = 14.2179(1) Å, c = 30.3492(3) Å, V = 5313.11(7) Å3, and Z = 3. In the structure of sergevanite, Ca and Mn are ordered in the six-membered ring of octahedra (at the sites M11 and M12), and Na dominates over Fe2+ at the M2 site. The strongest lines of the powder X-ray diffraction pattern [d, Å (I, %) (hkl)] are: 7.12 (70) (110), 5.711 (43) (202), 4.321 (72) (205), 3.806 (39) (033), 3.551 (39) (220, 027), 3.398 (39) (313), 2.978 (95) (), 2.855 (100) (404). Sergevanite is named after the Sergevan' River, which is near the discovery locality.

Centrosymmetric or Noncentrosymmetric? Case Study, Generalization and Structural Redetermination of Sr5Nb5O17

1998 ◽  
Vol 54 (4) ◽  
pp. 399-416 ◽  
Author(s):  
S. C. Abrahams ◽  
H. W. Schmalle ◽  
T. Williams ◽  
A. Reller ◽  
F. Lichtenberg ◽  
...  
Keyword(s):  
Niobium Oxide ◽  
The Novel ◽  
Physical Measurement ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
Data Set ◽  
Space Group ◽  
X Ray ◽  
Atomic Coordinates

The possibility that the structure of the novel semiconducting perovskite-related material strontium niobium oxide, Sr5Nb5O17, refined by Schmalle et al. [Acta Cryst. (1995), C51, 1243–1246] in space group Pnn2, might instead belong to space group Pnnm has been investigated following an analysis of the atomic coordinates that indicated the latter space group to be more likely. All I obs were carefully remeasured, first those within a hemisphere containing c *, then all that lay within the full sphere of reflection. Refinement was undertaken, with each of two different sets of weights, in each space group. Each data set was used under three limiting intensity conditions: I obs > 4σ(I obs), I obs > 2σ(I obs) and finally with all reflections, but setting magnitudes with I obs ≤ 0 equal to 0. Fourteen separate tests based only upon the X-ray diffraction data may be used to distinguish between Pnn2 and Pnnm. Nine tests favored the latter choice, four were indeterminate and one was not used. Seven further tests may be made on the basis of physical measurement; of these, three strongly indicated Pnnm, one was indeterminate and three could not be used. The evidence clearly suggests the space group is Pnnm. The use of all reflections, including those with negative magnitude set equal to zero, is essential to avoid ambiguity in the X-ray diffraction tests and achieve the highest reliability. Refinement with weights based on variances of Type A and Type B [Schwarzenbach et al. (1995). Acta Cryst. A51, 565–569] resulted in improved reliability compared with that obtained from a popular empirical weighting scheme. The revised structure differs in several respects from that published previously.

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