+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40269 | |||||||||
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Title | CryoEM map of a T=1 off-target state of design Oct(T=4)-3 | |||||||||
Map data | sharpened map from DeepEMhancer | |||||||||
Sample |
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Keywords | octahedral nanocage / T=4 / T=4 octahedra / nanomaterial / computational design / off-target / de novo / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.87 Å | |||||||||
Authors | Philomin A / Borst AJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking Authors: Lee S / Kibler RD / Hsia Y / Borst AJ / Philomin A / Kennedy MA / Stoddard B / Baker D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40269.map.gz | 91.7 MB | EMDB map data format | |
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Header (meta data) | emd-40269-v30.xml emd-40269.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40269_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_40269.png | 138 KB | ||
Filedesc metadata | emd-40269.cif.gz | 3.8 KB | ||
Others | emd_40269_additional_1.map.gz emd_40269_half_map_1.map.gz emd_40269_half_map_2.map.gz | 50.6 MB 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40269 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40269 | HTTPS FTP |
-Validation report
Summary document | emd_40269_validation.pdf.gz | 777.5 KB | Display | EMDB validaton report |
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Full document | emd_40269_full_validation.pdf.gz | 777.1 KB | Display | |
Data in XML | emd_40269_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_40269_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40269 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40269 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40269.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map from DeepEMhancer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.475 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map from final Non-Uniform Refinement
File | emd_40269_additional_1.map | ||||||||||||
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Annotation | unsharpened map from final Non-Uniform Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A from final Non-Uniform Refinement
File | emd_40269_half_map_1.map | ||||||||||||
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Annotation | half map A from final Non-Uniform Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B from final Non-Uniform Refinement
File | emd_40269_half_map_2.map | ||||||||||||
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Annotation | half map B from final Non-Uniform Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Oct(T=4)-3
Entire | Name: Oct(T=4)-3 |
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Components |
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-Supramolecule #1: Oct(T=4)-3
Supramolecule | Name: Oct(T=4)-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: A hierarchically designed T=4 octahedral nanocage |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 25mM Tris, 300mM NaCl |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm |