6ZHD

H11-H4 bound to Spike


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Z43 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined40.206
r_dihedral_angle_2_deg30.575
r_mcangle_it17.661
r_dihedral_angle_4_deg17.032
r_scbond_it14.587
r_dihedral_angle_3_deg13.385
r_mcbond_it10.223
r_dihedral_angle_1_deg5.968
r_angle_refined_deg1.264
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined40.206
r_dihedral_angle_2_deg30.575
r_mcangle_it17.661
r_dihedral_angle_4_deg17.032
r_scbond_it14.587
r_dihedral_angle_3_deg13.385
r_mcbond_it10.223
r_dihedral_angle_1_deg5.968
r_angle_refined_deg1.264
r_chiral_restr0.085
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Complex between Spike and nanobody H11-H4
Sample Components
Spike
nanobody H11-H4
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 90 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 81 % relative humidity and ambient temperature.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles126938
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsRelion
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6Z43)
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation
Overall B Value
Fitting Procedure
DetailsREFMAC was used via ccpem GUI
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)46
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 Magnification81000
Calibrated Magnification47170
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsEPU auto-function coma free correction
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO
IMAGE ACQUISITIONEPU2.6.1
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION3.08
FINAL EULER ASSIGNMENTRELION3.08
CLASSIFICATIONRELION
RECONSTRUCTIONRELION3.08
MODEL REFINEMENTREFMAC5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONRelion786392