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 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.

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 nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction

IUCrJ ◽  
2016 ◽  
Vol 3 (5) ◽  
pp. 300-308 ◽  
Author(s):  
Yifei Meng ◽  
Jian-Min Zuo
Keyword(s):  
Dimensional Space ◽  
Large Angle ◽  
Three Dimensional ◽  
Dark Field ◽  
Data Set ◽  
Angle Rotation ◽  
Diffraction Patterns ◽  
Scanning Electron ◽  
Three Dimensional Space

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can be extended to multiphase nanocrystalline materials as well. Thus, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.

Measuring procedure for the determination of the three-dimensional shape of dentures

1979 ◽  
Vol 42 (2) ◽  
pp. 149-153 ◽  
Author(s):  
Anton J. de Gee ◽  
Emmy C. ten Harkel ◽  
Carel L. Davidson
Keyword(s):  
Three Dimensional ◽  
Measuring Procedure ◽  
Dimensional Shape ◽  
Three Dimensional Shape

Determination of Tilt Parameters in Electron Diffraction Patterns of 3D-Microcrystals

1997 ◽  
Vol 3 (S2) ◽  
pp. 1049-1050
Author(s):  
E. Dimmeler ◽  
K.C. Holmes ◽  
R.R. Schröder
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Diffraction Spot ◽  
Spot Intensity ◽  
Crystal Face ◽  
Ewald Sphere ◽  
Exact Determination ◽  
Current Experimental Data ◽  
Diffraction Patterns

Electron crystallography of thin three-dimensional (3D) protein crystals requires very exact determination of tilt angles and spot profiles to obtain correct merging of diffraction spot amplitudes. The reciprocal lattice of 3D microcrystals consists of ellipsoidal spot profiles which are very extended in the direction normal to the crystal face (z*). To extrapolate from the intensity measured in a section to the total spot intensity, two features need to be known very exactly: 1. the orientation of reciprocal lattice relative to the Ewald sphere, 2. the 3D-shape of the spot cloud.Fig. 1 shows a tilt series of one frozen hydrated catalase crystal, in the order of recording. The third diffraction pattern gives the highest resolution because it is untilted and therefore the electrons have the shortest path length. In the current experimental data taken at 120 keV electron energy inelastic scattering within the crystal leads to a dramatic loss of elastic information in highly tilted patterns.

Structure-unit cell-based approach on three-dimensional representative braided preforms from four-step braiding: Experimental determination of effects of structure-process parameters on predetermined yarn path

2011 ◽  
Vol 82 (3) ◽  
pp. 220-241 ◽  
Author(s):  
Kadir Bilisik ◽  
Nesrin Sahbaz
Keyword(s):  
Cell Structure ◽  
Three Dimensional ◽  
Unit Cell ◽  
Number Of Layers ◽  
Cell Structures ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Surface Angle ◽  
Unit Cell Structure

The aim of this study was to understand the effects of braid pattern and the number of layers on three-dimensional (3D) braided unit cell structures. Various unit cell-based representative 3D braided preforms were developed. Data generated from these structures included unit cell dimensions, yarn angle, and yarn length in the unit cell structures. It was shown that braid patterns affected the 3D braided unit cell structures. The 1 × 1 braid pattern made fully interconnected integral 3D braided unit cell structures, whereas the 2 × 1 braid pattern created disconnected braid layers that were connected to the structures edges. When the number of layers increased, 3D braided unit cell thickness also increased. Braid pattern slightly affected the braider yarn angle, whereas the number of layers did not influence it. It was observed that the number of layers considerably affected the yarn length in the unit cell structure. Increasing the layer number from five to 10 layers created a yarn path in the unit cell edge regions called the ‘multilayer yarn length’. This yarn path was not observed below five-layer 3D braided unit cell structures. In jamming conditions, minimum jamming decreased the width of the unit cell structure, but maximum jamming increased its width. On the other hand, minimum jamming decreased the surface angle of the unit cell structure, whereas maximum jamming increased the surface angle. In addition, it was realized that jamming conditions influenced the density of the unit cell but did not affect the yarn length in the unit cell structures.

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.

scholarly journals Structure of catalase determined by MicroED

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Brent L Nannenga ◽  
Dan Shi ◽  
Johan Hattne ◽  
Francis E Reyes ◽  
Tamir Gonen
Keyword(s):  
Structure Determination ◽  
Three Dimensional ◽  
Bovine Liver ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Continuous Rotation ◽  
Bovine Liver Catalase ◽  
Diffraction Patterns ◽  
Atomic Analysis

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (<xref ref-type="bibr" rid="bib26">Shi et al., 2013</xref>). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

scholarly journals Study on creating the three-dimensional shape of apparel by thermal bonding of thermoplastic polyurethane film and vacuum forming molding

2020 ◽  
Vol 15 ◽  
pp. 155892501990015 ◽  
Author(s):  
Qiuyu Yu ◽  
Feng Zhou ◽  
Lingxiao Jing ◽  
Jing Song ◽  
Yi Xiang ◽  
...  
Keyword(s):  
Thermoplastic Polyurethane ◽  
Bonding Temperature ◽  
Three Dimensional ◽  
Fashion Design ◽  
Thermal Bonding ◽  
Vacuum Forming ◽  
Polyurethane Film ◽  
Dimensional Shape ◽  
Three Dimensional Shape

The shape of apparel is one of the most important elements in fashion design, for example, the three-dimensional shape of apparel can be quite creative and fashionable. The current technologies for creating the three-dimensional shape of apparel are many, but have their limitations in dealing with various fabrics, particularly light and soft fabrics. This article presents a new method to rapidly create three-dimensional shape of apparel for avoiding the aforementioned disadvantages. The method combines thermal bonding of thermoplastic polyurethane film and vacuum forming. In this study, 12 kinds of commercial fabrics were selected and then tested. All these fabrics were first bonded to thermoplastic polyurethane film and then rapidly applied to the vacuum forming machine to form the three-dimensional mold-like shape. This research analyzed the factors of molding a fabric to a good three-dimensional shape of apparel and the relative tests to be carried out for validating its stability for the selected fabric samples. There are two main contributions of this study. The first is to propose a more effective method for three-dimensional shape of apparel in fashion design. The second is to provide useful information for fabric selection and determination of bonding temperature in molding.

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