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Yorodumi- EMDB-19906: In situ nucleosome subtomogram average from Chlamydomonas reinhardtii -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19906 | |||||||||
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Title | In situ nucleosome subtomogram average from Chlamydomonas reinhardtii | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nucleosome / histone / cryo-et / chlamydomonas / chromatin / tomography / dna / in situ | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.65 Å | |||||||||
Authors | Michael AK / Righetto RD / Obr M / van der Stappen P / Lamm L / Khavnekar S / Kotecha A / Engel BD | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: To Be Published Title: In situ cryo-ET of Chlamydomonas reinhardtii prepared using cryo-plasma FIB milling Authors: Michael AK / Righetto RD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19906.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-19906-v30.xml emd-19906.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19906_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_19906.png | 42.8 KB | ||
Masks | emd_19906_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-19906.cif.gz | 4.4 KB | ||
Others | emd_19906_half_map_1.map.gz emd_19906_half_map_2.map.gz | 4 MB 4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19906 | HTTPS FTP |
-Validation report
Summary document | emd_19906_validation.pdf.gz | 833.4 KB | Display | EMDB validaton report |
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Full document | emd_19906_full_validation.pdf.gz | 832.9 KB | Display | |
Data in XML | emd_19906_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_19906_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19906 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19906 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19906.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.96 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19906_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19906_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19906_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chlamydomonas reinhardtii
Entire | Name: Chlamydomonas reinhardtii (plant) |
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Components |
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-Supramolecule #1: Chlamydomonas reinhardtii
Supramolecule | Name: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 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 |