scholarly journals 2.7 Å cryo-EM structure of vitrified M. musculus H-chain apoferritin from 200 keV “screening microscope”

2019 ◽  
Author(s):  
Farzad Hamdi ◽  
Christian Tüting ◽  
Dmitry A. Semchonok ◽  
Fotis L. Kyrilis ◽  
Annette Meister ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mechanical Stability ◽  
Objective Lens ◽  
List Type ◽  
Constant Power ◽  
Contrast Transfer Function ◽  
Microscopy Imaging ◽  
Detection Technology ◽  
High Emission ◽  
Solvent Molecules

AbstractHere we present the structure of mouse H-chain apoferritin at 2.7 Å (FSC=0.143) solved by single particle cryogenic electron microscopy (cryo-EM) using a 200 kV device. Data were collected using a compact, two-lens illumination system with a constant power objective lens, without the use of energy filters or aberration correctors. Coulomb potential maps reveal clear densities for main chain carbonyl oxygens, residue side chains (including alternative conformations) and bound solvent molecules. We argue that the advantages offered by (a) the high electronic and mechanical stability of the microscope, (b) the high emission stability and low beam energy spread of the high brightness Field Emission Gun (x-FEG), (c) direct electron detection technology and (d) particle-based Contrast Transfer Function (CTF) refinement have contributed to achieving resolution close to the Rayleigh limit. Overall, we show that basic electron optical settings for automated cryo-electron microscopy imaging, widely thought of as a “screening cryo-microscope”, can be used to determine structures approaching atomic resolution.HighlightsThe 2.7 Å structure of mouse apoferritin was solved using a 200 keV screening cryo-microscopeThe apoferritin reconstruction was resolved without an energy filter, aberration correctors, or constant-power condenser lensesComparison to available crystallographic and cryo-EM structures from high-end cryo-microscopes demonstrates consistency in resolved water molecules, metals and side chain orientationsAlthough radiation damage is more prominent at 200 keV compared to 300 keV, this type of instrumentation is more accessible to research laboratories due to its compactness and simplicity

Recent Progress and Plans in Computer-Controlled High Resolution Electron Microscopy

1990 ◽  
Vol 48 (1) ◽  
pp. 154-155
Author(s):  
W.J. de Ruijter ◽  
Peter Rez ◽  
David J. Smith
Keyword(s):  
Electron Microscopy ◽  
Digital Processing ◽  
High Resolution Electron Microscopy ◽  
Objective Lens ◽  
Linear Filter ◽  
Contrast Transfer Function ◽  
Image Displacement ◽  
Spatially Resolved ◽  
Wide Range ◽  
On Line

Digital computers are becoming widely recognized as standard accessories for electron microscopy. Due to instrumental innovations the emphasis in digital processing is shifting from off-line manipulation of electron micrographs to on-line image acquisition, analysis and microscope control. An on-line computer leads to better utilization of the instrument and, moreover, the flexibility of software control creates the possibility of a wide range of novel experiments, for example, based on temporal and spatially resolved acquisition of images or microdiffraction patterns. The instrumental resolution in electron microscopy is often restricted by a combination of specimen movement, radiation damage and improper microscope adjustment (where the settings of focus, objective lens stigmatism and especially beam alignment are most critical). We are investigating the possibility of proper microscope alignment based on computer induced tilt of the electron beam. Image details corresponding to specimen spacings larger than ∼20Å are produced mainly through amplitude contrast; an analysis based on geometric optics indicates that beam tilt causes a simple image displacement. Higher resolution detail is characterized by wave propagation through the optical system of the microscope and we find that beam tilt results in a dispersive image displacement, i.e. the displacement varies with spacing. This approach is valid for weak phase objects (such as amorphous thin films), where transfer is simply described by a linear filter (phase contrast transfer function) and for crystalline materials, where imaging is described in terms of dynamical scattering and non-linear imaging theory. In both cases beam tilt introduces image artefacts.

Instrumentation at the National Center for Electron Microscopy: The atomic resolution microscope

1983 ◽  
Vol 41 ◽  
pp. 310-311 ◽  
Author(s):  
R. Gronsky ◽  
G. Thomas
Keyword(s):  
Electron Microscopy ◽  
Atomic Resolution ◽  
Objective Lens ◽  
Contrast Transfer Function ◽  
Voltage Electron ◽  
Variable Voltage ◽  
New Instrument ◽  
Performance Specifications ◽  
Electron Microscopes ◽  
Point To Point

The Atomic Resolution Microscope (ARM) is one of two unique high voltage electron microscopes at the Lawrence Berkeley Laboratory's National Center for Electron Microscopy (NCEM). This paper reports on the latest results from this new instrument which was manufactured by JEOL, Ltd. to the performance specifications of the NCEM, delivered in January of 1983, and soon to be open to access by the entire microscopy community. Details of its history and development are given in reference 1; its performance specifications are reviewed below.Adopting as a design definition for resolution the first zero crossover of th% phase contrast transfer function at Scherzer defocus, the ARM (Fig. 1) maintains 1.7Å point-to-point resolution over its 400kV to 1000kV operating range. Consequently the microscope can be tuned to a voltage which is below the threshold for knock-on damage in a specimen and used to directly image its contiguous-atom structure. The key to this variable-voltage, high-resolution performance is a top-entry objective stage, which, in addition to ± 40° biaxial tilting, incorporates a height (Z)-control to alter specimen position within the objective lens.

The information limit of a 200kv field emission TEM

1995 ◽  
Vol 53 ◽  
pp. 586-587
Author(s):  
T. Kaneyama ◽  
M. Kawasaki ◽  
T. Tomita ◽  
T. Honda ◽  
M. Kersker
Keyword(s):  
Thin Film ◽  
Electron Microscope ◽  
Field Emission ◽  
Phase Contrast ◽  
Mechanical Stability ◽  
Power Supplies ◽  
Objective Lens ◽  
Operating Parameters ◽  
Contrast Transfer Function ◽  
Transmission Electron

The Point resolution of a transmission electron microscope is normally defined by the reciprocal of the spatial frequency of the first zero in the phase contrast transfer function at the Scherzer defocus condition. When a field emission gun (FEG) is used as the electron source, the information limit, that point at which the contrast beyond the first zero goes to zero contrast, becomes equally important. We have investigated the primary microscope parameters that affect the information limit.A 200kV FE-TEM (JEM-2010F) equipped with a ZrO/W shottkey emitter and Gatan Parallel EELS (PEELS) was used for the experiments. The aberration coefficients of the objective lens are Cs = 1mm and Cc = 1.4mm. The specimen used is an evaporated amorphous Ge thin film with small gold islands.The resolution performance of the microscope depends not only on the performance of the objective lens, the high voltage stability, stability of the lens and deflector power supplies, operating parameters of the FEG, and the overall mechanical stability of the microscopes.

Modification of Pineal Ultrastructure by Exogenous Hormones

1967 ◽  
Vol 25 ◽  
pp. 170-171
Author(s):  
R. A. Turner ◽  
A. E. Rodin ◽  
D. K. Roberts
Keyword(s):  
Electron Microscopy ◽  
Endoplasmic Reticulum ◽  
Rough Endoplasmic Reticulum ◽  
Estradiol Benzoate ◽  
Female Rats ◽  
List Type ◽  
Type Number ◽  
Pregnant Rats ◽  
Gonadal Atrophy ◽  
Pineal Ultrastructure

There have been many reports which establish a relationship between the pineal and sexual structures, including gonadal hypertrophy after pinealectomy, and gonadal atrophy after injection of pineal homogenates or of melatonin. In order to further delineate this relationship the pineals from 5 groups of female rats were studied by electron microscopy:ControlsPregnant ratsAfter 4 weekly injections of 0.1 mg. estradiol benzoate.After 8 daily injections of 150 mcgm. melatonin (pineal hormone).After 8 daily injections of 3 mg. serotonin (melatonin precursor).No ultrastructural differences were evident between the control, and the pregnancy and melatonin groups. However, the estradiol injected animals exhibited a marked increase in the amount and size of rough endoplasmic reticulum within the pineal cells.

High-resolution scanning electron microscopy (HRSEM) of mitochondria from various rat tissues

1988 ◽  
Vol 46 ◽  
pp. 14-15
Author(s):  
P.J. Lea ◽  
M.J. Hollenberg
Keyword(s):  
Electron Microscopy ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Rat Hepatocytes ◽  
Three Dimensions ◽  
Objective Lens ◽  
Rat Tissues ◽  
Thin Sections ◽  
Reconstruction Methods ◽  
Scanning Electron

Our current understanding of mitochondrial ultrastructure has been derived primarily from thin sections using transmission electron microscopy (TEM). This information has been extrapolated into three dimensions by artist's impressions (1) or serial sectioning techniques in combination with computer processing (2). The resolution of serial reconstruction methods is limited by section thickness whereas artist's impressions have obvious disadvantages.In contrast, the new techniques of HRSEM used in this study (3) offer the opportunity to view simultaneously both the internal and external structure of mitochondria directly in three dimensions and in detail.The tridimensional ultrastructure of mitochondria from rat hepatocytes, retinal (retinal pigment epithelium), renal (proximal convoluted tubule) and adrenal cortex cells were studied by HRSEM. The specimens were prepared by aldehyde-osmium fixation in combination with freeze cleavage followed by partial extraction of cytosol with a weak solution of osmium tetroxide (4). The specimens were examined with a Hitachi S-570 scanning electron microscope, resolution better than 30 nm, where the secondary electron detector is located in the column directly above the specimen inserted within the objective lens.

Comparison of Deterministic and Linear Cosine Spatial Filtering of Transmission Electron Micrographs

1972 ◽  
Vol 30 ◽  
pp. 596-597
Author(s):  
David A. Ansley
Keyword(s):  
Spherical Aberration ◽  
Focal Length ◽  
Chromatic Aberration ◽  
Spatial Filter ◽  
Operating Conditions ◽  
Objective Lens ◽  
List Type ◽  
Spatial Filters ◽  
Transmission Electron ◽  
Wide Range

The coherence of the electron flux of a transmission electron microscope (TEM) limits the direct application of deconvolution techniques which have been used successfully on unmanned spacecraft programs. The theory assumes noncoherent illumination. Deconvolution of a TEM micrograph will, therefore, in general produce spurious detail rather than improved resolution.A primary goal of our research is to study the performance of several types of linear spatial filters as a function of specimen contrast, phase, and coherence. We have, therefore, developed a one-dimensional analysis and plotting program to simulate a wide 'range of operating conditions of the TEM, including adjustment of the:(1) Specimen amplitude, phase, and separation(2) Illumination wavelength, half-angle, and tilt(3) Objective lens focal length and aperture width(4) Spherical aberration, defocus, and chromatic aberration focus shift(5) Detector gamma, additive, and multiplicative noise constants(6) Type of spatial filter: linear cosine, linear sine, or deterministic

New challenges to image processing posed by cryo-Electron microscopy of single particles

1991 ◽  
Vol 49 ◽  
pp. 422-423
Author(s):  
Joachim Frank
Keyword(s):  
Electron Microscopy ◽  
Phase Contrast ◽  
Particle Orientation ◽  
Single Particles ◽  
Contrast Transfer Function ◽  
Virtual Absence ◽  
Cryo Electron Microscopy ◽  
Spatial Frequencies ◽  
New Challenges ◽  
Particle Images

Compared with images of negatively stained single particle specimens, those obtained by cryo-electron microscopy have the following new features: (a) higher “signal” variability due to a higher variability of particle orientation; (b) reduced signal/noise ratio (S/N); (c) virtual absence of low-spatial-frequency information related to elastic scattering, due to the properties of the phase contrast transfer function (PCTF); and (d) reduced resolution due to the efforts of the microscopist to boost the PCTF at low spatial frequencies, in his attempt to obtain recognizable particle images.

Electron microscopy of keratinocytes cultured on a collagen substrate used as an allograft for the treatment of chronic wounds

1992 ◽  
Vol 50 (2) ◽  
pp. 1104-1105
Author(s):  
Debby A. Jennings ◽  
Michael J. Morykwas ◽  
Louis C. Argenta
Keyword(s):  
Electron Microscopy ◽  
Cell Suspension ◽  
Single Cell ◽  
Chronic Wounds ◽  
Mechanical Stability ◽  
Uv Light ◽  
Type I ◽  
Single Cell Suspension ◽  
Collagen Substrate ◽  
Dermal Collagen

Grafts of cultured allogenic or autogenic keratlnocytes have proven to be an effective treatment of chronic wounds and burns. This study utilized a collagen substrate for keratinocyte and fibroblast attachment. The substrate provided mechanical stability and augmented graft manipulation onto the wound bed. Graft integrity was confirmed by light and transmission electron microscopy.Bovine Type I dermal collagen sheets (100 μm thick) were crosslinked with 254 nm UV light (13.5 Joules/cm2) to improve mechanical properties and reduce degradation. A single cell suspension of third passage neonatal foreskin fibroblasts were plated onto the collagen. Five days later, a single cell suspension of first passage neonatal foreskin keratinocytes were plated on the opposite side of the collagen. The grafts were cultured for one month.The grafts were fixed in phosphate buffered 4% formaldehyde/1% glutaraldehyde for 24 hours. Graft pieces were then washed in 0.13 M phosphate buffer, post-fixed in 1% osmium tetroxide, dehydrated, and embedded in Polybed 812.

Defocus ramp correction in spot-scan imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 130-131
Author(s):  
Kenneth H. Downing
Keyword(s):  
Computer Control ◽  
Three Dimensional ◽  
Sufficient Accuracy ◽  
Objective Lens ◽  
Electron Crystallography ◽  
Contrast Transfer Function ◽  
Tilt Axis ◽  
Specimen Height ◽  
The Difference ◽  
Envelope Functions

Three-dimensional structures of a number of samples have been determined by electron crystallography. The procedures used in this work include recording images of fairly large areas of a specimen at high tilt angles. There is then a large defocus ramp across the image, and parts of the image are far out of focus. In the regions where the defocus is large, the contrast transfer function (CTF) varies rapidly across the image, especially at high resolution. Not only is the CTF then difficult to determine with sufficient accuracy to correct properly, but the image contrast is reduced by envelope functions which tend toward a low value at high defocus.We have combined computer control of the electron microscope with spot-scan imaging in order to eliminate most of the defocus ramp and its effects in the images of tilted specimens. In recording the spot-scan image, the beam is scanned along rows that are parallel to the tilt axis, so that along each row of spots the focus is constant. Between scan rows, the objective lens current is changed to correct for the difference in specimen height from one scan to the next.

Limits for high-resolution electron microscopy of inorganic materials?

1987 ◽  
Vol 45 ◽  
pp. 4-5
Author(s):  
David J. Smith
Keyword(s):  
Electron Microscopy ◽  
Spherical Aberration ◽  
High Resolution Electron Microscopy ◽  
Inorganic Materials ◽  
Atomic Scale ◽  
Resolution Limit ◽  
Contrast Transfer Function ◽  
Existing Problems ◽  
Resolution Electron ◽  
Electron Microscopes

The era of atomic-resolution electron microscopy has finally arrived. In virtually all inorganic materials, including oxides, metals, semiconductors and ceramics, it is possible to image individual atomic columns in low-index zone-axis projections. A whole host of important materials’ problems involving defects and departures from nonstoichiometry on the atomic scale are waiting to be tackled by the new generation of intermediate voltage (300-400keV) electron microscopes. In this review, some existing problems and limitations associated with imaging inorganic materials are briefly discussed. The more immediate problems encountered with organic and biological materials are considered elsewhere.Microscope resolution. It is less than a decade since the state-of-the-art, commercially available TEM was a 200kV instrument with a spherical aberration coefficient of 1.2mm, and an interpretable resolution limit (ie. first zero crossover of the contrast transfer function) of 2.5A.

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