scholarly journals Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

2013 ◽  
Vol 6 (1) ◽  
pp. 308 ◽  
Author(s):  
Mikael Elias ◽  
Dorothee Liebschner ◽  
Jurgen Koepke ◽  
Claude Lecomte ◽  
Benoit Guillot ◽  
...  
Keyword(s):  
High Resolution ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Diffraction Structure

scholarly journals Ultra-high resolution neutron and X-ray crystallography: structure of crambin

2014 ◽  
Vol 70 (a1) ◽  
pp. C1206-C1206
Author(s):  
Julian Chen ◽  
Bryant Hanson ◽  
S Fisher ◽  
Paul Langan ◽  
Andrey Kovalevsky ◽  
...  
Keyword(s):  
High Resolution ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Anisotropic Temperature ◽  
Exchange Patterns

Neutron diffraction data to 1.1 Å was collected on a crystal of the small protein crambin at the Protein Crystallography Station (PCS) at Los Alamos, the highest resolution neutron structure of a protein to date, and a technical benchmark for the instrument. 95 % of the hydrogen atoms in the protein structure were resolved. The data allowed for the refinement of anisotropic temperature factors for selected deuterium atoms within the protein. Hydrogen bonding networks ambiguous in room temperature, ultra-high resolution (0.84 Å) electron density maps are clarified in the nuclear density maps. The ultra-high resolution data also reveals unusual H/D exchange patterns and novel chemistry in the side chains and protein backbone. Complementary X-ray diffraction data was collected at 19-ID at the Advanced Photon Source, with extensive re-configuration of the beamline to allow for operation at higher energy settings.

Isomorphous replacement in electron diffraction of wet crystals of rat hemoglobin

1983 ◽  
Vol 41 ◽  
pp. 446-447
Author(s):  
William F. Tivol ◽  
Murray Vernon King ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Heavy Atom ◽  
Isomorphous Substitution ◽  
X Ray Diffraction ◽  
Salt Solutions ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Structure Factors ◽  
Diffraction Structure ◽  
The Mean

Feasibility of isomorphous substitution in electron diffraction is supported by a calculation of the mean alteration of the electron-diffraction structure factors for hemoglobin crystals caused by substituting two mercury atoms per molecule, following Green, Ingram & Perutz, but with allowance for the proportionality of f to Z3/4 for electron diffraction. This yields a mean net change in F of 12.5%, as contrasted with 22.8% for x-ray diffraction.Use of the hydration chamber in electron diffraction opens prospects for examining many proteins that yield only very thin crystals not suitable for x-ray diffraction. Examination in the wet state avoids treatments that could cause translocation of the heavy-atom labels or distortion of the crystal. Combined with low-fluence techniques, it enables study of the protein in a state as close to native as possible.We have undertaken a study of crystals of rat hemoglobin by electron diffraction in the wet state. Rat hemoglobin offers a certain advantage for hydration-chamber work over other hemoglobins in that it can be crystallized from distilled water instead of salt solutions.

A High Resolution Study of G.P. Zones in Aluminum - 4.2 at % Silver

1982 ◽  
Vol 40 ◽  
pp. 722-723 ◽  
Author(s):  
R. Gronsky
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
High Resolution ◽  
Computer Simulations ◽  
Structural Characteristics ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
Resolution Study

The phenomenon of clustering in Al-Ag alloys has been extensively studied since the early work of Guinierl, wherein the pre-precipitation state was characterized as an assembly of spherical, ordered, silver-rich G.P. zones. Subsequent x-ray and TEM investigations yielded results in general agreement with this model. However, serious discrepancies were later revealed by the detailed x-ray diffraction - based computer simulations of Gragg and Cohen, i.e., the silver-rich clusters were instead octahedral in shape and fully disordered, atleast below 170°C. The object of the present investigation is to examine directly the structural characteristics of G.P. zones in Al-Ag by high resolution transmission electron microscopy.

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.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

scholarly journals Dislocation Arrangement in a Thick LEO GaN Film on Sapphire

2000 ◽  
Vol 5 (S1) ◽  
pp. 97-103
Author(s):  
Kathleen A. Dunn ◽  
Susan E. Babcock ◽  
Donald S. Stone ◽  
Richard J. Matyi ◽  
Ling Zhang ◽  
...  
Keyword(s):  
High Resolution ◽  
Electron Diffraction ◽  
Threading Dislocations ◽  
X Ray Diffraction ◽  
Burgers Vector ◽  
X Ray ◽  
The Third ◽  
Dislocation Arrangement ◽  
Image Position ◽  
Gan Film

Diffraction-contrast TEM, focused probe electron diffraction, and high-resolution X-ray diffraction were used to characterize the dislocation arrangements in a 16µm thick coalesced GaN film grown by MOVPE LEO. As is commonly observed, the threading dislocations that are duplicated from the template above the window bend toward (0001). At the coalescence plane they bend back to lie along [0001] and thread to the surface. In addition, three other sets of dislocations were observed. The first set consists of a wall of parallel dislocations lying in the coalescence plane and nearly parallel to the substrate, with Burgers vector (b) in the (0001) plane. The second set is comprised of rectangular loops with b = 1/3 [110] (perpendicular to the coalescence boundary) which originate in the coalescence boundary and extend laterally into the film on the (100). The third set of dislocations threads laterally through the film along the [100] bar axis with 1/3<110>-type Burgers vectors These sets result in a dislocation density of ∼109 cm−2. High resolution X-ray reciprocal space maps indicate wing tilt of ∼0.5º.

Investigation of Residual Strains of the Second Kind in Plastically Deformed Metallic Materials

1994 ◽  
Vol 376 ◽  
Author(s):  
M. Vrána ◽  
P. Klimanek ◽  
T. Kschidock ◽  
P. Lukáš ◽  
P. Mikula
Keyword(s):  
High Resolution ◽  
Neutron Diffraction ◽  
Stacking Faults ◽  
Metallic Materials ◽  
Line Broadening ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Diffractometer ◽  
Residual Strains ◽  
Good Agreement

ABSTRACTInvestigation of strongly distorted crystal structures caused by dislocations, stacking-faults etc. in both plastically deformed f.c.c. and b.c.c. metallic materials was performed by the analysis of the neutron diffraction line broadening. Measurements were realized by means of the high resolution triple-axis neutron diffractometer equipped by bent Si perfect crystals as monochromator and analyzer at the NPI Řež. The substructure parameters obtained in this manner are in good agreement with the results of X-ray diffraction analysis.

The first proof of protonated anion tetrahedra in the tsumcorite-type compounds

2004 ◽  
Vol 68 (5) ◽  
pp. 757-767 ◽  
Author(s):  
T. Mihajlović ◽  
H. Effenberger
Keyword(s):  
Crystal Structure ◽  
Hydrothermal Synthesis ◽  
Single Crystal ◽  
Diffraction Data ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Synthetic Compounds ◽  
X Ray

AbstractHydrothermal synthesis produced the new compound SrCo2(AsO4)(AsO3OH)(OH)(H2O). The compound belongs to the tsumcorite group (natural and synthetic compounds with the general formula M(1)M(2)2(XO4)2(H2O,OH)2; M(1)1+,2+,3+ = Na, K, Rb, Ag, NH4, Ca, Pb, Bi, Tl; M(2)2+,3+ = Al, Mn3+, Fe3+, Co, Ni, Cu, Zn; and X5+,6+ = P, As, V, S, Se, Mo). It represents (1) the first Sr member, (2) the until now unknown [7]-coordination for the M(1) position, (3) the first proof of (partially) protonated arsenate groups in this group of compounds, and (4) a new structure variant.The crystal structure of the title compound was determined using single-crystal X-ray diffraction data. The compound is monoclinic, space group P21/a, with a = 9.139(2), b = 12.829(3), c = 7.522(2) Å, β = 114.33(3)°, V = 803.6(3) Å3, Z = 4 [wR2 = 0.065 for 3530 unique reflections]. The hydrogen atoms were located experimentally.

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