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Yorodumi- EMDB-14350: 64K CDS Apoferritin map reconstructed from 2.4K sub-tomograms wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14350 | |||||||||
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Title | 64K CDS Apoferritin map reconstructed from 2.4K sub-tomograms with emClarity | |||||||||
Map data | Sharpened emClarity map | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Clare DK | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: 2.9 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER COMMISSIONING SESSION CM26464-2 USING SUB-TOMOGRAM AVERAGING FROM 2.4K SUB-TOMOGRAMS Authors: Clare DK | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14350.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-14350-v30.xml emd-14350.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_14350.png | 304 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14350 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14350 | HTTPS FTP |
-Validation report
Summary document | emd_14350_validation.pdf.gz | 404.2 KB | Display | EMDB validaton report |
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Full document | emd_14350_full_validation.pdf.gz | 403.8 KB | Display | |
Data in XML | emd_14350_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_14350_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14350 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14350 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14350.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened emClarity map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.356 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : human Apoferritin
Entire | Name: human Apoferritin |
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Components |
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-Supramolecule #1: human Apoferritin
Supramolecule | Name: human Apoferritin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 / Details: Heavy chain |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM TCEP |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time of 2.5 seconds. |
Details | The apoferritin sample was applied to in-house graphene-coated Quantifoil r2/2 EM grid |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | Dose symmetric tilt series |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.5 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: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000 |
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
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 2400 |
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Extraction | Number tomograms: 2 / Number images used: 2400 / Reference model: from SPA / Method: emClarity / Software - Name: emClarity / Details: Template matching |
Final 3D classification | Software - Name: emClarity |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: emClarity |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |