EMD-8013

Single-particle
4.2 Å
EMD-8013
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Deposition: 15/12/2015
Map released: 27/01/2016
Last modified: 02/10/2019
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8013
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 5gao summary report (pdf.gz) Map and 5gao FULL report (pdf.gz)
EMICSS annotations (xml)

Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP

EMD-8013

Single-particle
4.2 Å
EMD-8013
3D View Gallery
Deposition: 15/12/2015
Map released: 27/01/2016
Last modified: 02/10/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.2 mg/mL
Buffer
pH: 7.9
Buffer components [1]:
Name Formula Concentration ChEBI
DTT - 1.0 mM -
Grid
Mesh: 400
Model: Quantifoil R1.2/1.3
Material: COPPER
Details: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS 6.0 nm
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.5 µm - 3.5 µm
Nominal magnification: 81000.0
Calibrated magnification: 35714.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Specialist optics
Energy filter
Name: GIF Quantum
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Frames per image: 1-20
Number of real images: 2477
Average exposure time: 16.0 s
Average electron dose per image: 38.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 4.2 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 140155
Software [1]
Name Version Details
RELION - -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-2966
Details:Startup model was 60 Angstrom low-pass filtered.
⦨ Initial angle assignment
Type: OTHER
Software [1]
Name Version Details
RELION - -
⦩ Final angle assignment
Type: OTHER
Software [1]
Name Version Details
RELION - -
Particle selection [1]
Selected Ref. model Method Software Details
473827 - - - -
CTF correction
Software [1]
Name Version Details
CTFFIND 4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Head Region of yeast spliceosomal U4/U6.U5 tri-snRNP.
⬡ Geometry
X Y Z
Dimensions 380 380 380
Origin 0 0 0
Spacing 380 380 380
Voxel size 1.43 Å 1.43 Å 1.43 Å
Contour list
Primary Level Source
True 0.02 AUTHOR