+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7346 | |||||||||
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Title | CRISPR RNA-guided surveillance complex, post-nicking | |||||||||
Map data | Cryo-EM map of Type 1-E Cascade-Cas3 complex at the state of post-NTS-nicking | |||||||||
Sample |
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Biological species | Thermobifida fusca (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Xiao Y / Luo M | |||||||||
Citation | Journal: To Be Published Title: CRISPR RNA-guided surveillance complex, post-nicking Authors: Xiao Y / Luo M / Liao M / Ke A | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7346.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-7346-v30.xml emd-7346.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_7346.png | 115.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7346 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7346 | HTTPS FTP |
-Validation report
Summary document | emd_7346_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_7346_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_7346_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7346 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7346 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7346.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Type 1-E Cascade-Cas3 complex at the state of post-NTS-nicking | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : CRISPR RNA-guided surveillance complex with Cas3 bound in its pos...
Entire | Name: CRISPR RNA-guided surveillance complex with Cas3 bound in its post-nicking state |
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Components |
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-Supramolecule #1: CRISPR RNA-guided surveillance complex with Cas3 bound in its pos...
Supramolecule | Name: CRISPR RNA-guided surveillance complex with Cas3 bound in its post-nicking state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12 |
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Source (natural) | Organism: Thermobifida fusca (bacteria) / Strain: YX |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pcdf |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.5 / Details: 10 mM Hepes, 150 mM NaCl, 5 mM DTT, pH 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80.0 K / Max: 105.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1428 / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.7 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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