EMD-4057

Single-particle
10.0 Å
EMD-4057
3D View Gallery
Deposition: 12/08/2016
Map released: 31/08/2016
Last modified: 11/12/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-4057
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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 5lj5 summary report (pdf.gz) Map and 5lj5 FULL report (pdf.gz)
EMICSS annotations (xml)

Structure of the yeast spliceosome immediately after branching. 3D class containing helicase module.

EMD-4057

Single-particle
10.0 Å
EMD-4057
3D View Gallery
Deposition: 12/08/2016
Map released: 31/08/2016
Last modified: 11/12/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.3 mg/mL
Buffer
pH: 7.8
Buffer components [3]:
Name Formula Concentration ChEBI
Hepes.KOH pH 7.8 - 20.0 millimolar -
Potassium chloride KCl 75.0 millimolar
EDTA - 250.0 micromolar -
Grid
Mesh: 400
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS 6.0 nm
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK III
Details: 3 microlitres sample were applied to the grid, left for 30 seconds and then blotted for 2.5-3.0 seconds before plunging..
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal defocus: 0.5 µm - 4.0 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 QUANTUM (4k x 4k)
Detector mode: SUPER-RESOLUTION
Frames per image: 1-20
Number of real images: 2213
Average exposure time: 0.8 s
Average electron dose per image: 2.0 e/Å2
Details: Total dose: 40 electrons/Angstrom^2 over 16 seconds. 20 movie frames collected at 1.25 frames per second.
Image processing [1]
Final reconstruction
Resolution: 10.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 15872
Software [1]
Name Version Details
RELION 1.4 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-6413
Details:Intron-lariat spliceosome complex low-pass filtered to 60 Angstrom
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
Particle selection [1]
Selected Ref. model Method Software Details
15872 - - - -
Final 3D classification
Software [1]
Name Version Details
RELION 1.4 -
CTF correction
Software [1]
Name Version Details
CTFFIND 4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
⬡ Geometry
X Y Z
Dimensions 412 412 412
Origin 0 0 0
Spacing 412 412 412
Voxel size 1.43 Å 1.43 Å 1.43 Å
Contour list
Primary Level Source
True 0.006 EMDB