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Yorodumi- EMDB-28742: 1.42 Angstrom Apoferritin structure determined using G1 Titan kri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28742 | |||||||||
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Title | 1.42 Angstrom Apoferritin structure determined using G1 Titan krios S-FEG operated at 300kV, zero loss imaging using Gatan BioQuantum energy filter operated at 10eV slit width and imaged using K2 camera. | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Keywords | Apoferritin / METAL BINDING PROTEIN | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.42 Å | |||||||||
Authors | VENUGOPAL H / RAMM G | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: To Be Published Title: Apoferritin structure from G1 Titan krios S-FEG system operated at 300kV, zero loss imaging using BioQuantum energy filter operated at 10eV slit width and imaged using K2 camera. Authors: Venugopal H / Ramm G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28742.map.gz | 168.2 MB | EMDB map data format | |
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Header (meta data) | emd-28742-v30.xml emd-28742.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28742_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_28742.png | 75.9 KB | ||
Masks | emd_28742_msk_1.map emd_28742_msk_2.map | 178 MB 178 MB | Mask map | |
Filedesc metadata | emd-28742.cif.gz | 4.4 KB | ||
Others | emd_28742_additional_1.map.gz emd_28742_half_map_1.map.gz emd_28742_half_map_2.map.gz | 89.6 MB 164.8 MB 164.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28742 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28742 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28742.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28742_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_28742_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Raw map
File | emd_28742_additional_1.map | ||||||||||||
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Annotation | Raw map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_28742_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_28742_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apoferritin
Entire | Name: ApoferritinFerritin |
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Components |
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-Supramolecule #1: Apoferritin
Supramolecule | Name: Apoferritin / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 480 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCl (pH 8.0), 150 mM NaCl |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3241 / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |