Artefact in 20Å-Resolution Electron Images of Negatively Stained Twodimensional Membrane Protein Crystals

1982 ◽  
Vol 40 ◽  
pp. 92-93
Author(s):  
Douglas L. Dorset ◽  
Barbara Moss
Keyword(s):  
Electron Scattering ◽  
Cross Correlation ◽  
Transmission Function ◽  
Group Symmetry ◽  
Asymmetric Structure ◽  
Object Model ◽  
Phase Object ◽  
Computing Systems ◽  
Resolution Electron ◽  
Plane Group

A number of computing systems devoted to the averaging of electron images of two-dimensional macromolecular crystalline arrays have facilitated the visualization of negatively-stained biological structures. Either by simulation of optical filtering techniques or, in more refined treatments, by cross-correlation averaging, an idealized representation of the repeating asymmetric structure unit is constructed, eliminating image distortions due to radiation damage, stain irregularities and, in the latter approach, imperfections and distortions in the unit cell repeat. In these analyses it is generally assumed that the electron scattering from the thin negativelystained object is well-approximated by a phase object model. Even when absorption effects are considered (i.e. “amplitude contrast“), the expansion of the transmission function, q(x,y)=exp (iσɸ (x,y)), does not exceed the first (kinematical) term. Furthermore, in reconstruction of electron images, kinematical phases are applied to diffraction amplitudes and obey the constraints of the plane group symmetry.

ASYMMETRIC-STRUCTURE ANALYSIS OF CARBON AND ENERGY MARKETS

Fractals ◽  
2016 ◽  
Vol 24 (01) ◽  
pp. 1650011 ◽  
Author(s):  
WEI XU ◽  
GUANGXI CAO
Keyword(s):  
Cross Correlation ◽  
Market Price ◽  
Energy Markets ◽  
Energy Market ◽  
Asymmetric Structure ◽  
Market Returns ◽  
Time Rate ◽  
Asymmetric Volatility ◽  
Volatility Transmission ◽  
Cross Correlation Analysis

This study aimed to investigate the asymmetric structure between the carbon and energy markets from two aspects of different trends (up or down) and volatility-transmission direction using asymmetric detrended cross-correlation analysis (DCCA) cross-correlation coefficient test, multifractal asymmetric DCCA (MF-ADCCA) method, asymmetric volatility-constrained correlation metric and time rate of information-flow approach. We sampled 1283 observations from January 2008 to December 2012 among pairs of carbon and energy markets for analysis. Empirical results show that the (1) asymmetric characteristic from the cross-correlation between carbon and returns in the energy markets is significant, (2) asymmetric cross-correlation between carbon and energy market price returns is persistent and multifractral and (3) volatility of the base assets of energy market returns is more influential to the base asset of the carbon market than that of the energy market.

Electron Decelerator for Improved CCD Performance In Intermediate Voltage Electron Microscopy

2000 ◽  
Vol 6 (S2) ◽  
pp. 734-735
Author(s):  
Kenneth H. Downing ◽  
Paola Favia ◽  
E. Mooney
Keyword(s):  
Electron Scattering ◽  
High Performance ◽  
Light Output ◽  
Ccd Cameras ◽  
Electronic Data Collection ◽  
Voltage Electron ◽  
Resolution Electron ◽  
Spread Function ◽  
Lens Coupling ◽  
Performance Tradeoff

There are many advantages of IVEMs over more conventional microscopes, all of which make it possible to obtain more accurate data at higher resolution. One significant drawback of higher accelerating voltages is degraded performance of the electron detector, a problem that is particularly serious with CCD cameras. At any voltage, one faces a tradeoff with the CCD performance between sensitivity and resolution. Electron scattering within the scintillator and its support broaden the point spread function, while the decreased scattering cross section at higher voltages decreases the light output from the scintillator. At voltages much above 100 kV these effects have been found to seriously limit CCD performance. With the trend towards electronic data collection and microscope automation, it is essential that a high performance detector be developed for the IVEM. One approach to optimizing the performance tradeoff employs lens coupling to improve resolution, at the expense of sensitivity.

Direct structure analysis in protein electron crystallography via the density histogram: deoxycholate-treated purple membrane

2000 ◽  
Vol 215 (5) ◽  
Author(s):  
Douglas L. Dorset
Keyword(s):  
Cross Correlation ◽  
Phase Error ◽  
Direct Methods ◽  
Sodium Deoxycholate ◽  
Purple Membrane ◽  
Mean Deviation ◽  
Plane Group ◽  
Density Histogram ◽  
The Mean ◽  
Experimental Density

The crystal structure of bacteriorhodopsin in purple membrane treated with sodium deoxycholate (plane group p3, a = 57.3 Å) was solved ab initio in projection from previously published electron diffraction amplitudes to 6.2 Å by direct methods for crystallographic phase determination. The best solution form the Sayre equation was identified by minimizing the skew properties of the cross-correlation of the experimental density histogram with the expected histogram. After Fourier refinement, the overall mean phase error is 43.3° for all 35 unique reflections of 16.9° for the 14 most intense maxima. For six clearly identified helix sites, the mean deviation of positions, when compared to the original model, was 0.7 Å.

Avoiding problems with hydrogen misplacement in reporting crystal structures

2013 ◽  
Vol 69 (8) ◽  
pp. 808-810 ◽  
Author(s):  
Ivan Bernal ◽  
Steven F. Watkins
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Quality Data ◽  
Computing Systems ◽  
High Quality Data ◽  
Positional Disorder ◽  
Donor Acceptor ◽  
Close Contacts

Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one-, two- or three-dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space-group symmetry. Yet some reported structures fail to include all possible donor–acceptor close contacts, or to seek H-atom electron densities associated with apparentD—H...Atrios, while some H-atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high-quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen-bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.

John Maxwell Cowley 1923 - 2004

2006 ◽  
Vol 17 (2) ◽  
pp. 227
Author(s):  
A. F. Moodie ◽  
J. C. H. Spence
Keyword(s):  
Electron Microscopy ◽  
Electron Diffraction ◽  
Electron Scattering ◽  
Scanning Transmission Electron Microscopy ◽  
High Resolution Electron Microscopy ◽  
Dynamical Theory ◽  
X Rays ◽  
Transmission Electron ◽  
Resolution Electron ◽  
Scanning Transmission

John Cowley contributed significantly to all of the fields that relate to electron diffraction and electron microscopy, and helped to found not a few of them. His name is associated in particular with n-beam dynamical theory, high-resolution electron microscopy, scanning transmission electron microscopy, instrumental design, and the application of the techniques of electron scattering to structure analysis. His experimental work was not, however, confined to the scattering of electrons: to take but one instance, his seminal work on the theory of short-range order was stimulated initially by his experiments using X-rays, and it was only later that he extended the technique to include electron diffraction. Finally, to all those who practise the techniques of scattering electrons, X-rays, or neutrons in the study of solids, liquids or gases, his book Diffraction Physics remains not only eminently readable but authoritative.

Crystal Packing of E.Coli Porin (Matrix Protein)

1981 ◽  
Vol 39 ◽  
pp. 42-43
Author(s):  
D.L. Dorset ◽  
A. Engel ◽  
R.M. Garavito ◽  
J.P. Rosenbusch
Keyword(s):  
Lipid Membranes ◽  
Matrix Protein ◽  
Crystal Packing ◽  
High Resolution Electron Microscopy ◽  
Strong Interactions ◽  
Electrical Measurements ◽  
Structure Packing ◽  
Negative Stain ◽  
Resolution Electron ◽  
Plane Group

Porin, a pore-forming protein spanning the outer membrane of E. coli (MW 36,500) has been isolated in homogeneous form after extraction in detergent. Electrical measurements on planar lipid membranes containing this protein indicate that it may be regarded as a paradigm of pore-forming transmembrane proteins. Therefore, a structural elucidation appears to be useful for correlating the pore geometry with the electrical measurements.Extraction of cells with ionic detergents, with or without removal of the peptidoglycan layer, has been monitored by Steven et al. using high resolution electron microscopy. Optical and computer reconstructions of the images indicated a trimeric structure packing in plane group p3 (a = 77 Å). Three dense patches of negative stain were tentatively assigned to the pores, an arrangement corroborated later by strong interactions among triplet channels observed in the conductance studies.

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