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Yorodumi- EMDB-39481: 2.08A Apoferritin Structure Solved Using an Indirect Scintillator... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39481 | |||||||||
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Title | 2.08A Apoferritin Structure Solved Using an Indirect Scintillator-Coupled CMOS Detector at 300 kV | |||||||||
Map data | FSC-weighted, shapened and masked map by PostProcess. | |||||||||
Sample |
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Keywords | apoferritin / ferritin / METAL BINDING PROTEIN | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.08 Å | |||||||||
Authors | Aramaki S / Yoshida Y / Tanihara T / Oyama K / Otsuki K / Terada Y / Matsunaga N / Ohdo S / Mayanagi K | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: High-Resolution Single Particle Analysis Using an Indirect Scintillator-Coupled CMOS Detector at 300 kV Authors: Aramaki S / Yoshida Y / Tanihara T / Oyama K / Otsuki K / Terada Y / Matsunaga N / Ohdo S / Mayanagi K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39481.map.gz | 13.9 MB | EMDB map data format | |
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Header (meta data) | emd-39481-v30.xml emd-39481.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39481_fsc.xml | 12.3 KB | Display | FSC data file |
Images | emd_39481.png | 140 KB | ||
Masks | emd_39481_msk_1.map | 22.2 MB | Mask map | |
Filedesc metadata | emd-39481.cif.gz | 4.6 KB | ||
Others | emd_39481_half_map_1.map.gz emd_39481_half_map_2.map.gz | 16.8 MB 16.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39481 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39481 | HTTPS FTP |
-Validation report
Summary document | emd_39481_validation.pdf.gz | 859.1 KB | Display | EMDB validaton report |
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Full document | emd_39481_full_validation.pdf.gz | 858.6 KB | Display | |
Data in XML | emd_39481_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_39481_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39481 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39481 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_39481.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | FSC-weighted, shapened and masked map by PostProcess. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_39481_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39481_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39481_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : apoferritin
Entire | Name: apoferritin |
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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: 440 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 11 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Phase plate: OTHER / Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1893 / Average exposure time: 2.3 sec. / Average electron dose: 92.9 e/Å2 / Details: TVIPS TemCam-XF416 (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 200000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |