scholarly journals A Method to Characterize and Correct Elliptical Distortion in Electron Diffraction Patterns

2008 ◽  
Vol 16 (3) ◽  
pp. 36-41
Author(s):  
Vincent D.-H. Hou ◽  
Du Li
Keyword(s):  
Image Processing ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
Objective Lens ◽  
Lens System ◽  
Electron Crystallography ◽  
Diffraction Ring ◽  
Diffraction Patterns ◽  
Instrument Level

One of the main obstacles to performing electron crystallography analysis in a TEM is that the acquired electron diffraction data often exhibits some form of distortion introduced by the lens system. Recognizing this problem, Capitani et al. has proposed a method to detect such distortion, which is primarily elliptical, by using a single crystal standard. Once such elliptical distortion is characterized, electron diffraction data acquired later can then be corrected by means of image processing. However, it may be desirable to correct such distortion at the instrument level. In this article, a different approach to measuring diffraction elliptical distortion is proposed by characterizing diffraction ring patterns and it is demonstrated that by varying the objective lens stigmation settings, it is possible to eliminate this elliptical distortion completely.

Effect of diffraction crystallography on HREM

2003 ◽  
Vol 218 (4) ◽  
Author(s):  
Fang-hua Li
Keyword(s):  
Image Processing ◽  
High Resolution ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Empirical Method ◽  
Crystal Defects ◽  
Electron Diffraction Data ◽  
Crystal Thickness ◽  
Resolution Electron

AbstractA simple image contrast theory in high-resolution electron microscopy (HREM) is introduced to demonstrate that below a certain critical crystal thickness the intensity of the Scherzer focus image is linear to the projected potential of an artificial crystal that is isomorphic to the examined one. It has become the theoretical base of electron crystallographic image processing techniques relying on the weak-phase-object approximation and kinematical diffraction. Two techniques of image processing are introduced. One of them aims at determining crystal structures by combining electron diffraction data and applying diffraction analysis methods. To reduce various kinds of electron diffraction intensity distortion the diffraction data are corrected by means of an empirical method set up by referring to the heavy atom method and Wilson statistic. The other one aims at revealing crystal defects at atomic resolution from the image taken with a medium-voltage field-emission high-resolution electron microscope. The dynamical effect is corrected by forcing the integral amplitudes of reflections in the diffractogram of image equal to the amplitudes of corresponding structure factors for the perfect crystal. The principle of the two techniques is briefly introduced, and examples of applications to crystal structure and defect determination are given.

A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction

2014 ◽  
Vol 47 (1) ◽  
pp. 215-221 ◽  
Author(s):  
Devinder Singh ◽  
Yifeng Yun ◽  
Wei Wan ◽  
Benjamin Grushko ◽  
Xiaodong Zou ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Basic Structure ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns

Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied forab initiostructure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al37.0(Co,Ni)15.5, denoted as PD2. RED shows that the crystal is F-centered, witha= 46.4,b= 64.6,c= 8.2 Å. However, as with other approximants in the PD series, the reflections with oddlindices are much weaker than those withleven, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parametersa= 23.2,b= 32.3,c= 4.1 Å and space groupPnmmhas been solved in the present study. The structure withc= 8.2 Å will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

scholarly journals Gently does it for submicron crystals

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Oliver B Zeldin ◽  
Axel T Brunger
Keyword(s):  
Electron Beam ◽  
Protein Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Large Numbers ◽  
Diffraction Patterns ◽  
Weak Electron

A protein structure has been refined with electron diffraction data obtained by using a very weak electron beam to collect large numbers of diffraction patterns from a few sub-micron-sized three-dimensional crystals.

Voltage dependence of the electron diffraction amplitudes in the ab initio analysis of copper perchlorophthalocyanine

1992 ◽  
Vol 50 (2) ◽  
pp. 1168-1169
Author(s):  
W.F. Tivol ◽  
J.N. Turner ◽  
D.L. Dorset
Keyword(s):  
Molecular Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Unit Cell ◽  
Electron Diffraction Data ◽  
Electron Microscopic ◽  
Heavy Atoms ◽  
C And N ◽  
Diffraction Patterns ◽  
Structure Research

Copper perchlorophthalocyanine has become a model compound for exploring the application of electron microscopic and diffraction methods in high resolution molecular structure research. Because of the scattering contrast between the Cu and Cl heavy atoms and the lighter C and N atoms, it was not possible to determine the structure with electron diffraction data obtained at 100 kV a number of years ago. Dynamical scattering all but obscures the detail in the diffraction data due to the unit cell Fourier transform. Studies at 500 kV had also determined that the electron microscopic images were influenced by dynamic scattering. Since our HVEM can be operated from 100 kV to 1.2 MV in 100 kV steps, we are studying the influence of accelerating voltage on our ability to determine atomic-level molecular structure.We recorded electron diffraction patterns from crystals epitaxially oriented on KCl and tilted 26.5° relative to the beam in order to align the c-axis of the unit cell along the beam direction.

Electron-diffraction patterns from frozen hydrate protein microcrystals: A new tool instructural studies

1994 ◽  
Vol 52 ◽  
pp. 102-103
Author(s):  
Christoph Burmester ◽  
Kenneth C. Holmes ◽  
Rasmus R. Schröder
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Atomic Resolution ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Phase Information ◽  
Isomorphous Replacement ◽  
Diffraction Patterns

Electron crystallography of 2D protein crystals can yield models with atomic resolution by taking Fourier amplitudes from electron diffraction and phase information from processed images. Imaging at atomic resolution is more difficult than the recording of corresponding electron diffraction patterns. Therefore attempts have been made to recover phase information from diffraction data from 2-D and 3-D crystals by the method of isomorphous replacement using heavy atom labelled protein crystals. These experiments, however, have so far not produced usable phase information, partly because of the large experimental error in the spot intensities. Here we present electron diffraction data obtained from frozen hydrated 3-D protein crystals with an energy-filter microscope and a specially constructed Image Plate scanner which are of considerably better crystallographic quality (as evidenced in much smaller values for the crystallographic R-factors Rsym and Rmerge) than those reported before. The quality of this data shows that the method of isomorphous replacement could indeed be used for phase determination for diffraction data obtained from 3-D microcrystals by electron diffraction.

EDIFF: a program for automated unit-cell determination and indexing of electron diffraction data

2011 ◽  
Vol 44 (5) ◽  
pp. 1132-1136 ◽  
Author(s):  
Linhua Jiang ◽  
Dilyana Georgieva ◽  
Jan Pieter Abrahams
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Unit Cell ◽  
Electron Diffraction Data ◽  
Cell Determination ◽  
Diffraction Patterns ◽  
Inorganic Molecules ◽  
User Friendly

EDIFFis a new user-friendly software suite for unit-cell determination of three-dimensional nanocrystals from randomly oriented electron diffraction patterns with unknown independent orientations. It can also be used for three-dimensional cell reconstruction from diffraction tilt series. In neither case is exact knowledge of the angular relationship between the patterns required. The unit cell can be validated and the crystal system assigned.EDIFFcan index the reflections in electron diffraction patterns. Thus,EDIFFcan be employed as a first step in reconstructing the three-dimensional atomic structure of organic and inorganic molecules and of proteins from diffraction data. An example illustrates the viability of theEDIFFapproach.

Electron Crystallography of Phthalocyanines

1999 ◽  
Vol 03 (07) ◽  
pp. 672-678 ◽  
Author(s):  
J. R. FRYER
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structural Information ◽  
High Resolution Electron Microscopy ◽  
Electron Diffraction Data ◽  
Electron Crystallography ◽  
Resolution Electron ◽  
Copper Phthalocyanines

It is shown that it is possible to obtain structural information from small (<100 nm) phthalocyanine crystals by using crystallographic direct phasing methods applied to electron diffraction data. This technique is both quantitative and does not suffer from the difficulties associated with high-resolution electron microscopy. Structural information has been obtained from both tetra- and octa chloro-copper phthalocyanines, and the results compared with the hydrogenated and perchloro members of the series.

Accurate Recording and Measurement of Electron Diffraction Data in Structural and Difference Fourier Studies of Proteins

2001 ◽  
Vol 7 (5) ◽  
pp. 407-417
Author(s):  
Kenneth H. Downing ◽  
Huilin Li
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Drug Binding ◽  
Electron Diffraction Data ◽  
Mathematical Basis ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Resolution Images ◽  
Diffraction Patterns ◽  
Difference Fourier

AbstractMany of the techniques that have been developed in X-ray crystallography are being applied in electron crystallographic studies of proteins. Electron crystallography has the advantage of measuring structure factor phases directly from high resolution images with an accuracy substantially higher than is common in X-ray crystallography. However, electron diffraction amplitudes are often not as precise as those obtained in X-ray work. We discuss here some approaches to maximizing the reliability of the diffraction amplitudes through choice of exposure and data processing schemes. With accurate measurement of diffraction data, Fourier difference methods can be used in electron crystallographic studies of small, localized changes of proteins that exist in two-dimensional crystals. The mathematical basis for the power of these methods in detecting small changes is reviewed. We then discuss several issues related to optimizing the quality of the diffraction data and derive an expression for the best exposure for recording diffraction patterns. An application of Fourier difference maps in localizing drug binding sites on the protein tubulin is discussed.

scholarly journals Three-dimensional electron crystallography of protein microcrystals

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Dan Shi ◽  
Brent L Nannenga ◽  
Matthew G Iadanza ◽  
Tamir Gonen
Keyword(s):  
Electron Diffraction ◽  
Protein Structures ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Electron Crystallography ◽  
Electron Dose ◽  
Tilt Series ◽  
Diffraction Patterns ◽  
A New Technique

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology.

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