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- EMDB-31413: Local map for Rd region of the red alga Porphyridium purpureum ph... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Local map for Rd region of the red alga Porphyridium purpureum phycobilisome in Middle Light | |||||||||
![]() | Rd | |||||||||
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Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ma JF / Sui S-F | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structural basis for light acclimation in phycobilisome light harvesting systems systems in Porphyridium purpureum Authors: Dodson EJ / Ma J / Suissa Szlejf M / Maroudas-Sklare N / Paltiel Y / Adir N / Sun S / Sui SF / Keren N | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
Images | ![]() | 118.7 KB | ||
Filedesc metadata | ![]() | 4.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Rd | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.066 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : phycobilisome
Entire | Name: phycobilisome![]() |
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Components |
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-Supramolecule #1: phycobilisome
Supramolecule | Name: phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14700 kDa/nm |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 Component:
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 2 | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 18 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Quantum ER |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 2 / Number real images: 6438 / Average exposure time: 8.2 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 315046 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta) |
Final 3D classification | Number classes: 5 / Avg.num./class: 87399 / Software - Name: RELION (ver. 3.1beta) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 87399 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 62.05 / Target criteria: 0,99 |