scholarly journals Gap junction structures: Analysis of the x-ray diffraction data

1977 ◽  
Vol 74 (2) ◽  
pp. 629-645 ◽  
Author(s):  
L Makowski ◽  
DLD Caspar ◽  
WC Phillips ◽  
DA Goodenough
Keyword(s):  
Electron Microscope ◽  
Gap Junction ◽  
Electron Density ◽  
Diffraction Data ◽  
Pair Correlation ◽  
Hexagonal Lattice ◽  
Chemical Data ◽  
X Ray Diffraction ◽  
Interference Function ◽  
X Ray

Models for the spatial distribution of protein, lipid and water in gap junction structures have been constructed from the results of the analysis of X-ray diffraction data described here and the electron microscope and chemical data presented in the preceding paper (Caspar, D. L. D., D. A. Goodenough, L. Makowski, and W.C. Phillips. 1977. 74:605-628). The continuous intensity distribution on the meridian of the X-ray diffraction pattern was measured, and corrected for the effects of the partially ordered stacking and partial orientation of the junctions in the X-ray specimens. The electron density distribution in the direction perpendicular to the plane of the junction was calculated from the meridional intensity data. Determination of the interference function for the stacking of the junctions improved the accuracy of the electron density profile. The pair-correlation function, which provides information about the packing of junctions in the specimen, was calculated from the interference function. The intensities of the hexagonal lattice reflections on the equator of the X-ray pattern were used in coordination with the electron microscope data to calculate to the two-dimensional electron density projection onto the plane of the membrane. Differences in the structure of the connexons as seen in the meridional profile and equatorial projections were shown to be correlated to changes in lattice constant. The parts of the junction structure which are variable have been distinguished from the invariant parts by comparison of the X-ray data from different specimens. The combination of these results with electron microscope and chemical data provides low resolution three- dimensional representations of the structures of gap junctions.

scholarly journals Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

2017 ◽  
Vol 73 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Anatoly A. Udovenko ◽  
Alexander A. Karabtsov ◽  
Natalia M. Laptash
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Central Atom ◽  
X Ray Diffraction ◽  
Dynamic Nature ◽  
Orientational Disorder ◽  
High Quality ◽  
Structural Units ◽  
X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

Experimental electron density study of 1,2,4-triazole at 15 K. A comparison with ab initio-calculations

1997 ◽  
Vol 212 (3) ◽  
Author(s):  
P. Fuhrmann ◽  
T. Koritsánszky ◽  
P. Luger
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Electron Density ◽  
Diffraction Data ◽  
Topological Properties ◽  
X Ray Diffraction ◽  
X Ray ◽  
Experimental Electron Density ◽  
Density Study

AbstractTopological properties and the Laplacian function of the electron density of 1,2,4-triazole have been determined from X-ray diffraction data collected at 15 K. 1,2,4-Triazole, C

scholarly journals ELECTRON MICROSCOPE AND X-RAY DIFFRACTION STUDIES OF THE EFFECTS OF DEHYDRATION ON THE STRUCTURE OF NERVE MYELIN

1960 ◽  
Vol 8 (1) ◽  
pp. 13-29 ◽  
Author(s):  
J. B. Finean
Keyword(s):  
Electron Microscope ◽  
Electron Micrographs ◽  
Diffraction Data ◽  
Intermediate Stage ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dense Line ◽  
Tissue Shrinkage ◽  
Frog Sciatic Nerve ◽  
Electron Microscope Data

The dehydration of frog sciatic nerve has been studied by allowing specimens to become partially or fully dried before fixation and preparation for electron microscopy. Low magnification electron micrographs of OsO4-fixed preparations showed marked tissue shrinkage which could be correlated quantitatively with the loss of water during the preliminary drying. KMnO4-fixation appeared to cause a rehydration of the dried tissue. Higher magnification electron micrographs of the OsO4-fixed preparations showed a sequence of modifications of the myelin layers which could be correlated with changes in the small-angle x-ray diffraction data which were recorded during drying. An intermediate stage of drying was characterised by a partial collapse of layers and a disappearance of the intraperiod dense line in some regions of the myelin sheath. Continuity between collapsed and non-collapsed layers was maintained throughout the sheath. The fully dried preparation showed two main modifications of the myelin layers. In many regions the layers (principal layers) resembled those of normal preparations, but showed an intensification and frequently a doubling of the intraperiod dense line. In addition, there was a very extensive system of fine (40 A periodicity) dense layers, some of which could be demonstrated to be continuous with the principal layers. In such cases it was observed that two of the fine layers were related to each principal layer. The correlation between diffraction data and electron microscope data is discussed, and some speculations are made concerning the molecular significance of the observations.

Electron-density Fourier maps of an untwinnedYBa2Cu3O6.877single crystal by x-ray-diffraction data

1993 ◽  
Vol 48 (14) ◽  
pp. 10638-10641 ◽  
Author(s):  
J. D. Sullivan ◽  
P. Bordet ◽  
M. Marezio ◽  
K. Takenaka ◽  
S. Uchida
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data

2014 ◽  
Vol 70 (5) ◽  
pp. 1491-1497 ◽  
Author(s):  
Jimin Wang ◽  
Richard A. Wing
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Uniform Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Correlation ◽  
Atomic Models ◽  
Weak Intensity

Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperatureBfactors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individualBfactors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent mergingRfactors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes throughde novoNCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.

A combined model of electron density and lattice dynamics refined against elastic diffraction data. Thermodynamic properties of crystalline L-alanine

2020 ◽  
Vol 76 (1) ◽  
pp. 32-44 ◽  
Author(s):  
Ioana Sovago ◽  
Anna A. Hoser ◽  
Anders Ø. Madsen
Keyword(s):  
Dft Calculations ◽  
Electron Density ◽  
Normal Mode ◽  
Diffraction Data ◽  
Lattice Dynamics ◽  
Phonon Dispersion ◽  
Form Factors ◽  
X Ray Diffraction ◽  
Crystalline Materials ◽  
X Ray

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion – phonons – in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol−1 K−1 of the calorimetric measurements, in the temperature range 10–300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.

Scanning Electron Microscope Studies on the Morphology of Zeolites Occurring in Bentonites

1974 ◽  
Vol 32 ◽  
pp. 458-459
Author(s):  
Paul J. Jehn ◽  
Necip Güven ◽  
J. Franklin Bailey
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Volcanic Material ◽  
Scanning Electron

Zeolites occur as major constituents in several bentonite samples from Japan and Argentina. They are believed to be formed by devitrification of volcanic material. X-ray diffraction data indicate that the major zeolite phases in these samples are heulandite Ca(Al2Si7O18)·6H2O, clinoptilolite Na2(Al2Si7O18)6H2O, mordenite (Na2K2Ca) (Al2Si10O24)·7H2O, analcite Na(AlSi2O6)·H2O and possibly epistilbite Ca(Al2Si6O16)·5H2O.

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