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.

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.

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.

Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters

2012 ◽  
Vol 68 (5) ◽  
pp. 536-546 ◽  
Author(s):  
Sebastian Schlitt ◽  
Tatiana E. Gorelik ◽  
Andrew A. Stewart ◽  
Elmar Schömer ◽  
Thorsten Raasch ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Unit Cell ◽  
Electron Diffraction Data ◽  
Unit Cell Parameters ◽  
Clustering Techniques ◽  
Cell Parameters

scholarly journals MicroED: Three Dimensional Electron Crystallography of Protein Micro-Crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C1063-C1063
Author(s):  
Tamir Gonen
Keyword(s):  
Electron Diffraction ◽  
Protein Structures ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Molecular Replacement ◽  
Electron Crystallography ◽  
Electron Dose ◽  
Tilt Series ◽  
Diffraction Patterns

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 1.7Å 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 - 10and 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 2.9Å resolution. In this seminar I will present our initial proof of principle study and highlight the major advances since the first publication.

scholarly journals Procedure and Computer Programs for the Structure Determination of Gaseous Molecules from Electron Diffraction Data.

1969 ◽  
Vol 23 ◽  
pp. 3224-3234 ◽  
Author(s):  
B. Andersen ◽  
H. M. Seip ◽  
T. G. Strand ◽  
R. Stølevik ◽  
Gunner Borch ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Computer Programs ◽  
Electron Diffraction Data
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