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Yorodumi- EMDB-9865: The 1.54 A resolution structure of apoferritin by CRYOARM300 with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9865 | |||||||||
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Title | The 1.54 A resolution structure of apoferritin by CRYOARM300 with Cold-FEG | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.54 Å | |||||||||
Authors | Kato T / Nakane T / Makino F / Terahara N / Yonekura K / Namba K | |||||||||
Citation | Journal: Microsc Microanal / Year: 2019 Title: CryoTEM with a Cold Field Emission Gun That Moves Structural Biology into a New Stage Authors: Kato T / Makino F / Nakane T / Terahara N / Kaneko T / Shimizu Y / Motoki S / Ishikawa I / Yonekura K / Namba K | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9865.map.gz | 324.2 MB | EMDB map data format | |
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Header (meta data) | emd-9865-v30.xml emd-9865.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9865_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_9865.png | 104.5 KB | ||
Masks | emd_9865_msk_1.map | 347.6 MB | Mask map | |
Others | emd_9865_half_map_1.map.gz emd_9865_half_map_2.map.gz | 271.7 MB 271.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9865 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9865 | HTTPS FTP |
-Validation report
Summary document | emd_9865_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_9865_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_9865_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9865 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9865 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
EM raw data | EMPIAR-10248 (Title: The 1.54 Å structure of Apoferritin by CRYOARM300 with cold-FEG Data size: 145.9 Data #1: Unaligned multi-frame micrographs of Apoferritin recorded by CRYOARM300 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9865.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.495 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_9865_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: nominal 0.5 A/px, calibrated 0.495 A/px
File | emd_9865_half_map_1.map | ||||||||||||
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Annotation | nominal 0.5 A/px, calibrated 0.495 A/px | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: nominal 0.5 A/px, calibrated 0.495 A/px
File | emd_9865_half_map_2.map | ||||||||||||
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Annotation | nominal 0.5 A/px, calibrated 0.495 A/px | ||||||||||||
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) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 504 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | |||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Both side glow discharged | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Temperature | Min: 100.4 K / Max: 100.4 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Details | JEM-Z300FSC |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 947 / Average exposure time: 10.0 sec. / Average electron dose: 88.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.167 µm / Calibrated defocus min: 0.315 µm / Calibrated magnification: 101000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: NITROGEN |