7Z9Q

CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZHD 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.835
r_lrange_it17.501
r_lrange_other17.501
r_dihedral_angle_4_deg15.466
r_dihedral_angle_3_deg13.488
r_mcangle_it7.486
r_mcangle_other7.485
r_scangle_it7.406
r_scangle_other7.406
r_dihedral_angle_1_deg6.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.835
r_lrange_it17.501
r_lrange_other17.501
r_dihedral_angle_4_deg15.466
r_dihedral_angle_3_deg13.488
r_mcangle_it7.486
r_mcangle_other7.485
r_scangle_it7.406
r_scangle_other7.406
r_dihedral_angle_1_deg6.354
r_mcbond_it4.245
r_mcbond_other4.245
r_scbond_it4.011
r_scbond_other4.011
r_angle_other_deg1.544
r_angle_refined_deg1.469
r_nbd_refined0.206
r_symmetry_nbd_other0.192
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.16
r_ncsr_local_group_20.103
r_ncsr_local_group_10.101
r_chiral_restr0.099
r_ncsr_local_group_30.087
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.068
r_bond_other_d0.031
r_ext_dist_refined_d0.031
r_ncsr_local_group_40.021
r_ncsr_local_group_50.021
r_ncsr_local_group_60.021
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.003
Sample
Complex between Spike and nanobody H11-A10
Sample Components
Spike glycoprotein trimer
Nanobody H11-A10
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentSPOTITON
Cryogen NameETHANE
Sample Vitrification DetailsSPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-dischar ...SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 260 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 80% relative humidity and ambient temperature.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles305820
Reported Resolution (Å)3.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6ZHD, 6ZHD, 6ZHD)
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)51.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1500
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 Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsEPU auto-function coma free correction
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera
MODEL FITTINGCoot
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTRELION3.08
FINAL EULER ASSIGNMENTRELION3.08
CLASSIFICATIONRELION3.08
RECONSTRUCTIONRELION3.08
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION3264123