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CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZHD
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.835 r_lrange_it 17.501 r_lrange_other 17.501 r_dihedral_angle_4_deg 15.466 r_dihedral_angle_3_deg 13.488 r_mcangle_it 7.486 r_mcangle_other 7.485 r_scangle_it 7.406 r_scangle_other 7.406 r_dihedral_angle_1_deg 6.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.835 r_lrange_it 17.501 r_lrange_other 17.501 r_dihedral_angle_4_deg 15.466 r_dihedral_angle_3_deg 13.488 r_mcangle_it 7.486 r_mcangle_other 7.485 r_scangle_it 7.406 r_scangle_other 7.406 r_dihedral_angle_1_deg 6.354 r_mcbond_it 4.245 r_mcbond_other 4.245 r_scbond_it 4.011 r_scbond_other 4.011 r_angle_other_deg 1.544 r_angle_refined_deg 1.469 r_nbd_refined 0.206 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.16 r_ncsr_local_group_2 0.103 r_ncsr_local_group_1 0.101 r_chiral_restr 0.099 r_ncsr_local_group_3 0.087 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.068 r_bond_other_d 0.031 r_ext_dist_refined_d 0.031 r_ncsr_local_group_4 0.021 r_ncsr_local_group_5 0.021 r_ncsr_local_group_6 0.021 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Sample Complex between Spike and nanobody H11-A10 Sample Components Spike glycoprotein trimer Nanobody H11-A10
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument SPOTITON Cryogen Name ETHANE Sample Vitrification Details 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-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 Method SINGLE PARTICLE Number of Particles 305820 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6ZHD, 6ZHD, 6ZHD) Refinement Space RECIPROCAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 51.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details EPU auto-function coma free correction
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION Gctf MODEL FITTING UCSF Chimera MODEL FITTING Coot MODEL REFINEMENT REFMAC INITIAL EULER ASSIGNMENT RELION 3.08 FINAL EULER ASSIGNMENT RELION 3.08 CLASSIFICATION RELION 3.08 RECONSTRUCTION RELION 3.08
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3264123