EMD-4436

Single-particle
3.8 Å
EMD-4436
3D View Gallery
Deposition: 26/11/2018
Map released: 06/11/2019
Last modified: 13/11/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-4436
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Five-fold symmetrized map of native bacteriophage P68

EMD-4436

Single-particle
3.8 Å
EMD-4436
3D View Gallery
Deposition: 26/11/2018
Map released: 06/11/2019
Last modified: 13/11/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 2 mg/mL
Buffer
pH: 8.0
Buffer components [3]:
Name Formula Concentration ChEBI
Tris(hydroxymethyl)aminomethane Tris 50.0 mM
Calcium chloride CaCl 10.0 mM
Sodium chloride NaCl 10.0 mM
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 293 K
Instrument: FEI VITROBOT MARK IV
Details: Blot time 2s; blot force -2; 3.6 ul of sample.
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.001 µm - 0.003 µm
Nominal magnification: 75000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: FEI FALCON II (4k x 4k)
Detector mode: INTEGRATING
Dimensions: 4096 pixel x 4096 pixel
Sampling interval: 1.063 µm
Frames per image: 1-7
Number of grids: 2
Number of real images: 2891
Average exposure time: 1.0 s
Average electron dose per image: 21.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.8 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 28826
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C5
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-1222
Details:The initial model was scaled and clipped in EMAN2 to match the dimensions of phage P68. command: e2proc3d.py --clip=600 --scale=0.73
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
Particle selection [1]
Selected Ref. model Method Software Details
37218 - - - -
Final 3D classification
Number of classes: 3
Avg. number of members per classes: 11210.0
Software [1]
Name Version Details
RELION 2.1 -
CTF correction
Software [1]
Name Version Details
CTFFIND 4.0 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Five-fold symmetrized map of native bacteriophage P68
⬡ Geometry
X Y Z
Dimensions 600 600 600
Origin -300 -300 -300
Spacing 600 600 600
Voxel size 1.063 Å 1.063 Å 1.063 Å
Contour list
Primary Level Source
True 0.1 AUTHOR