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 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.

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.

SIR2011: a new package for crystal structure determination and refinement

2012 ◽  
Vol 45 (2) ◽  
pp. 357-361 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Protein Structures ◽  
Three Dimensional ◽  
Molecular Geometry ◽  
Electron Diffraction Data ◽  
Medium Size ◽  
Molecular Replacement ◽  
Density Maps ◽  
Difficult Cases

SIR2011, the successor ofSIR2004, is the latest program of theSIRsuite. It can solveab initiocrystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities:e.g.a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometryviasimulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

Global least-squares determination of Eulerian angles from single electron diffraction patterns of tilted crystals

2000 ◽  
Vol 33 (4) ◽  
pp. 1088-1101 ◽  
Author(s):  
Eva Dimmeler ◽  
Rasmus R. Schröder
Keyword(s):  
Electron Diffraction ◽  
Least Squares ◽  
Three Dimensional ◽  
Test Sample ◽  
Single Electron ◽  
Dimensional Structure ◽  
Diffraction Spot ◽  
Linear Fit ◽  
Diffraction Patterns

Three-dimensional structure determination using electron diffraction of crystalline samples necessitates the determination of the Eulerian angles of tilted samples. For experimental tilt series, even with approximately known tilt, the resolution of the final three-dimensional reconstructions is reduced as a result of the large errors of the refined tilt angles and crystal axes positions. The presented new least-squares procedure determines the orientation of the crystal with very high accuracy from a single electron diffraction pattern. Instead of evaluating the averaged pattern geometry, each diffraction spot position is individually included in an analytical non-linear fit. This procedure is very stable against potential experimental errors, as demonstrated by Monte Carlo simulations. As a test sample, a three-dimensional microcrystal of an organic crystal compound was used. Contrary to the conventional method, which produced erroneous Miller indices for some reflections, the indexing obtained with the new algorithm was more consistent for each individual pattern. Preliminary data from frozen hydrated protein crystals, the samples of which are beam sensitive and for which only a few patterns can be recorded from a single crystal, indicate that the new angle determination promises to be particularly beneficial under such conditions.

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.

Determination of lattice-transform density profiles for multilayered three-dimensional microcrystals in electron crystallography

2000 ◽  
Vol 33 (4) ◽  
pp. 1102-1112 ◽  
Author(s):  
Eva Dimmeler ◽  
Oliver Vossen ◽  
Rasmus R. Schröder
Keyword(s):  
Three Dimensional ◽  
Electron Crystallography ◽  
Data Set ◽  
Density Profiles ◽  
New Correlation ◽  
Diffraction Geometry ◽  
Dimensional Shape ◽  
Diffraction Patterns ◽  
Unit Cell Dimensions

Electron crystallography on multilayered three-dimensional microcrystals has been limited in application by the need to define precisely the three-dimensional shape of the diffraction density profiles. A new method is presented here to obtain this profile from experimental spot positions which are shifted in a characteristic way from the expected Bragg positions. While the Bragg positions are defined by the diffraction geometry, the characteristic shift additionally depends on the density profile in Fourier space. In general, these two effects are intermingled. A new correlation approach is presented which uses characteristic shift patterns to separate these effects. This technique also allows the determination of all three crystallographic unit-cell dimensions from a single tilted electron diffraction pattern. It was tested on simulated diffraction patterns and applied to experimental data of frozen hydrated crystals of the protein catalase. Since multilayered catalase crystals with different numbers of crystallographic layers were studied, an inhomogeneous data set had to be evaluated. Processing of such data is now possible using the new correlation approach.

scholarly journals On the Completeness of Three-Dimensional Electron Diffraction Data for Structural Analysis of Metal-Organic Frameworks

2021 ◽  
Author(s):  
Meng Ge ◽  
Taimin Yang ◽  
Yanzhi Wang ◽  
Francesco Carraro ◽  
Weibin Liang ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Electron Diffraction ◽  
Metal Organic Frameworks ◽  
Three Dimensional ◽  
Accurate Method ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
The Past ◽  
Metal Organic

Three-dimensional electron diffraction (3DED) has been proven as an effective and accurate method for structure determination of nano-sized crystals. In the past decade, the crystal structures of various new complex...

Multiple isomorphous replacement for phase determination in protein crystals

1995 ◽  
Vol 53 ◽  
pp. 856-857
Author(s):  
Christoph Burmester ◽  
Kenneth C. Holmes ◽  
Rasmus R. Schröder
Keyword(s):  
Electron Diffraction ◽  
Heavy Atom ◽  
Atomic Resolution ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Phase Information ◽  
Electron Dose ◽  
Isomorphous Replacement ◽  
Resolution Electron ◽  
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 high resolution electron diffraction patterns. Therefore attempts have been made to retrieve phase information from diffraction from heavy atom labelled protein crystals. The expected differences between native and labelled crystals are small, therefore a high experimental accuracy is necessary. This is achieved by the use of energy filter TEM and image plates, as dicussed in. Here we present electron diffraction data obtained from frozen hydrated 3D protein crystals with an energy filter microspcope and a specially designed image plate scanner. Data were recorded for the native crystal as well as for two different heavy atom derivatives. Differences between the native and the derivate forms can be detected and are significant.Electron diffraction patterns from frozen hydrated catalase crystals were recorded on an EFTEM Zeiss 912 Ω (120kV, zero loss mode, energy width ΔE=10eV, electron dose 5 e-/A2) using image plates and a quasi confocal scanner readout.

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.

Sign in / Sign up

Export Citation Format

Share Document