EMD-22944

Single-particle
16.8 Å
EMD-22944
3D View Gallery
Deposition: 04/11/2020
Map released: 18/11/2020
Last modified: 01/09/2021
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-22944
Download
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)

Negative stain electron microscopy reconstruction of NTD-directed Fab DH1050.1 in complex with hexapro SARS-CoV-2 spike ectodomain

EMD-22944

Single-particle
16.8 Å
EMD-22944
3D View Gallery
Deposition: 04/11/2020
Map released: 18/11/2020
Last modified: 01/09/2021
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.1 mg/mL
Buffer
pH: 7.4
Buffer components [3]:
Name Formula Concentration ChEBI
Sodium chloride NaCl 150.0 mM
HEPES buffer - 20.0 mM -
Glycerol - 5.0 g/dL -
Staining
Type: NEGATIVE
Material: Uranyl Formate
Details: Samples were diluted to 0.1 mg/mL in 20 mM HEPES buffer, pH 7.4, with 5% glycerol, 150 mM NaCl, and 7.5 mM glutaraldehyde. After 5 minute incubation at room temperature, sufficient 1 M Tris stock, pH 7.4, was added to a final concentration of 75 mM Tris to quench unreacted glutaraldehyde, and was then incubated 5 minutes. Sample was then applied to a carbon film over 400 mesh copper EM grids that had been glow-discharged, incubated 1 minute, and then stained with 2% uranyl formate.
Grid
Mesh: 300
Model: Homemade
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS 5.0 nm
Microscopy [1]
Microscope: FEI/PHILIPS EM420
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.4 µm - 1.5 µm
Nominal magnification: 82000.0
Specimen holder model: SIDE ENTRY, EUCENTRIC
Alignment procedure: BASIC
Image Recording [1]
Detector model: OTHER
Dimensions: 2048 pixel x 2048 pixel
Sampling interval: 33.0 µm
Number of grids: 1
Number of real images: 249
Average exposure time: 0.5 s
Average electron dose per image: 32.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 16.8 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 11158
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 3.0 -
Startup model [1]
Type: PDB ENTRY
PDB model: 6VSB
Details:Map of PDB 6VSB was generated within Chimera using the molmap function at 15 Angstrom resolution and 4.02 Angstrom grid spacing. This map was low-pass filtered to 60 Angstrom before initiating refinements.
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0 -
Particle selection [1]
Selected Ref. model Method Software Details
267753 - - - -
Final 3D classification
Number of classes: 9
Avg. number of members per classes: 13040.0
Software [1]
Name Version Details
RELION 3.0 -
CTF correction
Software [1]
Name Version Details
CTFFIND 4.1.8 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Final sharpened map of NTD-directed Fab DH1050.1 in complex with hexapro SARS-CoV-2 spike ectodomain
⬡ Geometry
X Y Z
Dimensions 96 96 96
Origin 0 0 0
Spacing 96 96 96
Voxel size 4.02 Å 4.02 Å 4.02 Å
Contour list
Primary Level Source
True 0.05 AUTHOR