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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | G1 nucleosome gyre proximal | |||||||||
![]() | G1 nucleosome gyre proximal class 1 | |||||||||
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![]() | Cell / RPE-1 / nucleus / nucleosome / NUCLEAR PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 30.6 Å | |||||||||
![]() | Chen JK / Cai S / Liu T / Ruan W / Ng CT / Shi J / Surana U / Gan L | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nanoscale analysis of human G1 and metaphase chromatin in situ Authors: Chen JK / Liu T / Cai S / Ruan W / Ng CT / Shi J / Surana U / Gan L | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 741.2 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.4 KB 22.4 KB | Display Display | ![]() |
Images | ![]() | 49.8 KB | ||
Filedesc metadata | ![]() | 4.6 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 742.8 KB 741.8 KB 742.4 KB 742 KB 740.7 KB 740 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 616 KB | Display | ![]() |
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Full document | ![]() | 615.6 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | G1 nucleosome gyre proximal class 1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 6.766 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: G1 nucleosome gyre proximal class 2
File | emd_36994_additional_1.map | ||||||||||||
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Annotation | G1 nucleosome gyre proximal class 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: G1 nucleosome gyre proximal class 3
File | emd_36994_additional_2.map | ||||||||||||
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Annotation | G1 nucleosome gyre proximal class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: G1 nucleosome gyre proximal class 4
File | emd_36994_additional_3.map | ||||||||||||
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Annotation | G1 nucleosome gyre proximal class 4 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: G1 nucleosome gyre proximal class 5
File | emd_36994_additional_4.map | ||||||||||||
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Annotation | G1 nucleosome gyre proximal class 5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_36994_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_36994_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nucleosome gyre proximal from RPE-1
Entire | Name: Nucleosome gyre proximal from RPE-1 |
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Components |
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-Supramolecule #1: Nucleosome gyre proximal from RPE-1
Supramolecule | Name: Nucleosome gyre proximal from RPE-1 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 30369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.1 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 2016 |
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Extraction | Number tomograms: 21 / Number images used: 165964 / Reference model: Featureless cylinder / Method: Template matching |
Final 3D classification | Number classes: 1 / Software - Name: RELION (ver. 3.0.8) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8) |