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- EMDB-41938: CryoEM map of horse spleen apoferritin determined for benchmarkin... -
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Open data
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Basic information
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Title | CryoEM map of horse spleen apoferritin determined for benchmarking square and rectangular apertures for cryo-EM (Gatan K3 rectangular beam) | |||||||||
![]() | Main map, reconstructed from cryo-TEM data recorded with a rectangular aperture. Sharpened with B-factor 47.7 A. | |||||||||
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![]() | Apo-ferritin / METAL BINDING PROTEIN | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.81 Å | |||||||||
![]() | Brown HG / Hanssen E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Square condenser apertures for square cameras in low-dose transmission electron microscopy. Authors: Hamish G Brown / Dan Smith / Benjamin C Wardle / Eric Hanssen / ![]() Abstract: In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam- ...In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 483.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.8 KB | Display | ![]() |
Images | ![]() | 191.6 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 4.7 KB | ||
Others | ![]() ![]() | 474.4 MB 474.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Main map, reconstructed from cryo-TEM data recorded with a rectangular aperture. Sharpened with B-factor 47.7 A. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.655 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_41938_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_41938_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Apoferritin from equine spleen
Entire | Name: Apoferritin from equine spleen |
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Components |
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-Supramolecule #1: Apoferritin from equine spleen
Supramolecule | Name: Apoferritin from equine spleen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Purchased from Sigma Aldrich product number A3641 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 481.2 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 35 mg/mL |
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Buffer | pH: 7.4 / Component - Formula: PBS |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Details: Quorum Glocube |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
Details | Solution purchased from Sigma Aldrich and no further purification |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 3111 / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |