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Yorodumi- EMDB-24099: Map of commercially purchased Apoferritin after 2 freeze-thaw cycles -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24099 | |||||||||
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Title | Map of commercially purchased Apoferritin after 2 freeze-thaw cycles | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Equus ferus (tarpan) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.38 Å | |||||||||
Authors | Parvate AD / Moser TJ / Evans JE | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structure of commercially purchased Apoferritin after 2 freeze thaw cycles Authors: Parvate AD / Moser TJ / Evans JE | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24099.map.gz | 229.5 MB | EMDB map data format | |
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Header (meta data) | emd-24099-v30.xml emd-24099.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_24099.png | 73.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24099 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24099 | HTTPS FTP |
-Validation report
Summary document | emd_24099_validation.pdf.gz | 467.9 KB | Display | EMDB validaton report |
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Full document | emd_24099_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | emd_24099_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_24099_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24099 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24099 | HTTPS FTP |
-Related structure data
Related structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24099.map.gz / Format: CCP4 / Size: 244.1 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: 0.3398 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-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 Details: Commercially purchased fully assembled protein complex |
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Source (natural) | Organism: Equus ferus (tarpan) |
Molecular weight | Theoretical: 444 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7 Details: Solutions made fresh and filtered with 0.22 micron filter for sterility. |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: 2 s blot. |
Details | Sample was monodisperse and suspended in TBS. Sample underwent 2 rounds of freeze thaw prior to plunge freezing |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Phase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 1944 / Average exposure time: 1.56 sec. / Average electron dose: 50.13 e/Å2 |
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 FIELD / Cs: 2.7 mm / Nominal defocus max: -1.3 µm / Nominal defocus min: -0.3 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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