9ML6 | pdb_00009ml6

Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C9 Fab


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7UZD 
experimental modelPDB 7UZ4 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d8.3642
f_angle_d0.5737
f_chiral_restr0.0457
f_plane_restr0.0038
f_bond_d0.0027
Sample
SARS-CoV-2 Spike 6P in complex with M8b-C9 Fab
Sample Components
Severe acute respiratory syndrome coronavirus 2 spike glycoprotein
M8b-C9 Fab
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles132671
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7UZD, 7SC1)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value90
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.3
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.3
MODEL FITTINGUCSF Chimera1.18
INITIAL EULER ASSIGNMENTcryoSPARC4.3
FINAL EULER ASSIGNMENTcryoSPARC4.3
CLASSIFICATIONcryoSPARC4.3
RECONSTRUCTIONcryoSPARC4.3
MODEL REFINEMENTPHENIX1.21.2_5419
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1159077