7OR9

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NX6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M amino acids (Glu, Ala, Gly, Lys, Ser), 0.1 M MES/imidazole pH 6.5, 10% (w/v) PEG 20000 and 20% (v/v) PEG MME 550.
Crystal Properties
Matthews coefficientSolvent content
3.0659.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.73α = 90
b = 114.47β = 90
c = 177.93γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.347086.20.10.030.99916.811.65325152.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.380.3480.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7NX62.3457.231.3453154265386.070.19530.19350.229661.39
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.494
f_angle_d0.5406
f_chiral_restr0.0425
f_plane_restr0.0045
f_bond_d0.0022
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8047
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms67

Software

Software
Software NamePurpose
PHENIXrefinement
GDAdata collection
xia2data reduction
xia2data scaling
PHASERphasing