EMD-3631

Single-particle
3.1 Å
EMD-3631
3D View Gallery
Deposition: 10/03/2017
Map released: 21/06/2017
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-3631
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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 5nej summary report (pdf.gz) Map and 5nej FULL report (pdf.gz)
EMICSS annotations (xml)

CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa

EMD-3631

Single-particle
3.1 Å
EMD-3631
3D View Gallery
Deposition: 10/03/2017
Map released: 21/06/2017
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.5 mg/mL
Buffer
pH: 8.0
Buffer components [1]:
Name Formula Concentration ChEBI
HEPES - 50.0 mM -
Grid
Mesh: 300
Model: C-flat-2/1
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Time: 15 s
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON HOLEY 5.0
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 294 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.0 mm
Nominal defocus: 1.0 µm - 4.0 µm
Nominal magnification: 160000.0
Calibrated magnification: 37037.0
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Temperature
Minimum: 70.0 K
Maximum: 70.0 K
Specialist optics
Energy filter
Name: GIF
Lower energy threshold: 0 eV
Upper energy threshold: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 3838 pixel x 3710 pixel
Frames per image: 2-20
Number of grids: 1
Number of real images: 360
Average exposure time: 5.0 s
Average electron dose per image: 18.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.1 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 13483
Algorithm: BACK PROJECTION
Software [1]
Name Version Details
RELION 1.3 -
Startup model [1]
Type: PDB ENTRY
PDB model: 1BBT
⦨ Initial angle assignment
Type: COMMON LINE
Software [1]
Name Version Details
RELION 1.3 -
⦩ Final angle assignment
Type: COMMON LINE
Software [1]
Name Version Details
RELION 1.3 -
Particle selection [1]
Selected Ref. model Method Software Details
13483 - - - -
Final 3D classification
Software [1]
Name Version Details
RELION 1.3 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa
⬡ Geometry
X Y Z
Origin -199 -200 -200
Dimensions (px) 400 400 400
Dimensions (Å) 540.0 540.0 540.0
Voxel size (Å) 1.35 1.35 1.35
Contour list
Primary Level Source
True 0.037 AUTHOR