EMD-0336

Single-particle
3.68 Å
EMD-0336
3D View Gallery
Deposition: 16/11/2018
Map released: 19/12/2018
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-0336
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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 6n3q summary report (pdf.gz) Map and 6n3q FULL report (pdf.gz)
EMICSS annotations (xml)

Cryo-EM structure of the yeast Sec complex

EMD-0336

Single-particle
3.68 Å
EMD-0336
3D View Gallery
Deposition: 16/11/2018
Map released: 19/12/2018
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 5 mg/mL
Buffer
pH: 7.5
Grid
Mesh: 400
Model: Quantifoil R1.2/1.3
Material: GOLD
Pretreatment
Type: PLASMA CLEANING
Time: 20 s
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TALOS ARCTICA
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.8 µm - 2.4 µm
Nominal magnification: 43103.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Average exposure time: 8.0 s
Average electron dose per image: 50.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.68 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 172531
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
CryoSPARC 2.0.27 -
Startup model [1]
Type: OTHER
Details:Ab initio reconstruction by cryoSPARC
⦨ Initial angle assignment
Type: RANDOM ASSIGNMENT
Software [1]
Name Version Details
CryoSPARC 2.0.27 -
⦩ Final angle assignment
Type: OTHER
Software [1]
Name Version Details
CryoSPARC 2.0.27 -
Particle selection [1]
Selected Ref. model Method Software Details
358961 - - - -
Final 3D classification
Number of classes: 3
Software [1]
Name Version Details
CryoSPARC 2.0.27 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Sharpened full map
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 256 256 256
Dimensions (Å) 296.96 296.96 296.96
Voxel size (Å) 1.16 1.16 1.16
Contour list
Primary Level Source
True 0.42 AUTHOR