EMD-7808

Single-particle
3.45 Å
EMD-7808
3D View Gallery
Deposition: 22/04/2018
Map released: 20/06/2018
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-7808
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 6d6q summary report (pdf.gz) Map and 6d6q FULL report (pdf.gz)
EMICSS annotations (xml)

Human nuclear exosome-MTR4 RNA complex - overall reconstruction

EMD-7808

Single-particle
3.45 Å
EMD-7808
3D View Gallery
Deposition: 22/04/2018
Map released: 20/06/2018
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 1.0 mg/mL
Details: Sample was monodisperse upon elution from gel filtration prior to vitrification.
Buffer
pH: 8.0
Buffer components [6]:
Name Formula Concentration ChEBI
Tris-HCl - 20.0 mM -
Sodium chloride NaCl 100.0 mM
Magnesium chloride MgCl2 0.5 mM
AMPPNP - 2.0 mM -
BME - 1.0 mM -
Chapso - 0.05 % -
Grid
Model: Quantifoil R2/2
Material: GOLD
Pretreatment
Type: GLOW DISCHARGE
Time: 60 s
Atmosphere: AIR
Pressure: 0.037 kPa
Vitrification
Cryogen name: ETHANE
Chamber temperature: 298 K
Instrument: FEI VITROBOT MARK IV
Details: 30 sec wait time, 2.5 sec blot time.
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Number of real images: 1439
Average electron dose per image: 85.23 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.45 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 122703
Software [1]
Name Version Details
RELION 2.1b1 -
Startup model [1]
Type: NONE
Details:Ab initio model determination
⦨ Initial angle assignment
Type: RANDOM ASSIGNMENT
Software [1]
Name Version Details
CryoSPARC 0.6.1 From 0.6.1 to 0.6.5
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 2.1b1 -
Particle selection [1]
Selected Ref. model Method Software Details
278185 - - - -
Final 3D classification
Number of classes: 4
Avg. number of members per classes: 271036.0
Software [1]
Name Version Details
RELION 2.1b1 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Overall reconstruction for human nuclear exosome-MTR4 helicase complex
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 384 384 384
Dimensions (Å) 410.88 410.88 410.88
Voxel size (Å) 1.07 1.07 1.07
Contour list
Primary Level Source
True 0.025 AUTHOR