Steric Parameters of Conformationally Flexible Ligands from X-ray Structural Data. 2. P(OR)3Ligands in Multiple Ligand Environments

2001 ◽  
Vol 20 (6) ◽  
pp. 1210-1215 ◽  
Author(s):  
Jeremy M. Smith ◽  
Neil J. Coville
Keyword(s):  
Structural Data ◽  
X Ray ◽  
Flexible Ligands ◽  
Multiple Ligand

Steric Parameters of Conformationally Flexible Ligands from X-ray Structural Data. 1. P(OR)3Ligands in Equivalent Ligand Environments

2000 ◽  
Vol 19 (25) ◽  
pp. 5273-5280 ◽  
Author(s):  
Jeremy M. Smith ◽  
Neil J. Coville ◽  
Leanne M. Cook ◽  
Jan C. A. Boeyens
Keyword(s):  
Structural Data ◽  
X Ray ◽  
Equivalent Ligand ◽  
Flexible Ligands

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 Gem-Quality Tourmaline from LCT Pegmatite in Adamello Massif, Central Southern Alps, Italy: An Investigation of Its Mineralogy, Crystallography and 3D Inclusions

Minerals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 593 ◽  
Author(s):  
Valeria Diella ◽  
Federico Pezzotta ◽  
Rosangela Bocchio ◽  
Nicoletta Marinoni ◽  
Fernando Cámara ◽  
...  
Keyword(s):  
Rare Earth ◽  
Manganese Content ◽  
Diffraction Method ◽  
Structural Data ◽  
Massif Central ◽  
X Ray ◽  
Geological Processes ◽  
Chemical Studies ◽  
Micro Tomography ◽  
Cation Sites

In the early 2000s, an exceptional discovery of gem-quality multi-coloured tourmalines, hosted in Litium-Cesium-Tantalum (LCT) pegmatites, was made in the Adamello Massif, Italy. Gem-quality tourmalines had never been found before in the Alps, and this new pegmatitic deposit is of particular interest and worthy of a detailed characterization. We studied a suite of faceted samples by classical gemmological methods, and fragments were studied with Synchrotron X-ray computed micro-tomography, which evidenced the occurrence of inclusions, cracks and voids. Electron Microprobe combined with Laser Ablation analyses were performed to determine major, minor and trace element contents. Selected samples were analysed by single crystal X-ray diffraction method. The specimens range in colour from colourless to yellow, pink, orange, light blue, green, amber, brownish-pink, purple and black. Chemically, the tourmalines range from fluor-elbaite to fluor-liddicoatite and rossmanite: these chemical changes occur in the same sample and affect the colour. Rare Earth Elements (REE) vary from 30 to 130 ppm with steep Light Rare Earth Elemts (LREE)-enriched patterns and a negative Eu-anomaly. Structural data confirmed the elbaitic composition and showed that high manganese content may induce the local static disorder at the O(1) anion site, coordinating the Y cation sites occupied, on average, by Li, Al and Mn2+ in equal proportions, confirming previous findings. In addition to the gemmological value, the crystal-chemical studies of tourmalines are unanimously considered to be a sensitive recorder of the geological processes leading to their formation, and therefore, this study may contribute to understanding the evolution of the pegmatites related to the intrusion of the Adamello pluton.

Relationship between Solid-State31P NMR Parameters and X-ray Structural Data in Some Zinc Phosphonates

1997 ◽  
Vol 9 (1) ◽  
pp. 6-7 ◽  
Author(s):  
Dominique Massiot ◽  
Stéphanie Drumel ◽  
Pascal Janvier ◽  
Martine Bujoli-Doeuff ◽  
Bruno Bujoli
Keyword(s):  
Structural Data ◽  
X Ray ◽  
Nmr Parameters

scholarly journals The Rosetta all-atom energy function for macromolecular modeling and design

2017 ◽  
Author(s):  
Rebecca F. Alford ◽  
Andrew Leaver-Fay ◽  
Jeliazko R. Jeliazkov ◽  
Matthew J. O'Meara ◽  
Frank P. DiMaio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Energy Function ◽  
Crystal Structure Data ◽  
Structural Data ◽  
X Ray ◽  
The Past ◽  
Biomolecular Modeling ◽  
Macromolecular Modeling ◽  
Atom Energy

AbstractOver the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta’s success is the energy function: amodel parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, beta_nov15. Applying these concepts,we explain how to use Rosetta energies to identify and analyze the features of biomolecular models.Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.

Relationship Between New Structural Data on Clinoptilolite and Its Behaviour in Ion-Exchange and Heating

1979 ◽  
Vol 34 (2) ◽  
pp. 248-250 ◽  
Author(s):  
Iliana M. Galabova
Keyword(s):  
Ion Exchange ◽  
Structural Data ◽  
X Ray ◽  
Good Accord ◽  
Low Degrees

Abstract Low degrees of removal of K in ion-exchange as well as alterations of relative intensities of (0k0) X-ray reflections under heating have been found for clinoptilolite. These observations are in good accord with the newly provided structural data of clinoptilolite

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.

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