EMD-8729

Single-particle
10.5 Å
EMD-8729
3D View Gallery
Deposition: 13/05/2017
Map released: 26/07/2017
Last modified: 29/01/2020
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-8729
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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)
EMICSS annotations (xml)

Cryo-EM reconstruction of the HIV-1 BG505 SOSIP.664 Env trimer in complex with soluble CD4 (D1-D2)

EMD-8729

Single-particle
10.5 Å
EMD-8729
3D View Gallery
Deposition: 13/05/2017
Map released: 26/07/2017
Last modified: 29/01/2020
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 1 mg/mL
Buffer
pH: 7.4
Buffer components [3]:
Name Formula Concentration ChEBI
Sodium chloride NaCl 150.0 mM
Tris C4H11NO3 50.0 mM
DDM - 1.125 mM -
Grid
Mesh: 400
Model: C-flat
Material: COPPER
Pretreatment
Type: PLASMA CLEANING
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 50%
Chamber temperature: 277 K
Instrument: HOMEMADE PLUNGER
Details: 5 microliters of the complex was incubated with 3 microliters of a fresh 1.8 mM DDM solution. A 3 microliter aliquot of the complex was applied to a C-Flat grid (CF-2/2-4C, Electron Microscopy Sciences, Protochips, Inc.) which had been plasma cleaned for 5 seconds using a mixture of Ar/O2 (Gatan Solarus 950 Plasma system), blotted off, and then immediately plunged into liquid ethane using a manual freeze plunger..
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: 100.0 µm
Nominal CS: 2.7 mm
Calibrated defocus: 1.0 µm - 4.0 µm
Nominal magnification: 22500.0
Calibrated magnification: 38167.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Temperature
Minimum: 90.0 K
Maximum: 90.0 K
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Sampling interval: 5.0 µm
Frames per image: 1-28
Number of grids: 1
Average exposure time: 5.6 s
Average electron dose per image: 32.0 e/Å2
Details: Individual frames were gain-corrected, aligned, and summed using MotionCor.
Image processing [1]
Final reconstruction
Resolution: 10.5 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 1754
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C3
Software [1]
Name Version Details
FREALIGN 9.11 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: Common lines model using OptiMod
Details:An initial model was generated directly from the class averages using OptiMod.
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Angular sampling: 7.5 degrees
Details: Relion 3D classification, auto mode
Software [1]
Name Version Details
RELION 1.3 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Details: Frealign 3D classification and refinement
Software [1]
Name Version Details
FREALIGN 9.11 -
Final 3D classification
Software [1]
Name Version Details
FREALIGN 3.11 -
CTF correction
Details: Performed internally in Relion and Frealign
Software [1]
Name Version Details
CTFFIND 3 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: BG505 SOSIP trimer bound to sCD4
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 128 128 128
Dimensions (Å) 335.36 335.36 335.36
Voxel size (Å) 2.62 2.62 2.62
Contour list
Primary Level Source
True 0.11 AUTHOR