7BEK

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.62940.15 M (NH4)2SO4, 0.1 M Tris pH 7.6 and 14.6% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.2261.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.02α = 90
b = 149.41β = 90
c = 145.49γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-09-09MSINGLE 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
12.0451.499.90.1180.0330.99913.113.45774747.04
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)
12.042.080.3450.5

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-VALUE7EBJ2.0442.711.3357631289899.670.20080.19970.219562.73
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_d12.7349
f_angle_d0.562
f_chiral_restr0.0432
f_plane_restr0.0043
f_bond_d0.0024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4802
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms101

Software

Software
Software NamePurpose
Cootmodel building
PHENIXrefinement
GDAdata collection
xia2data reduction
xia2data scaling
PHASERphasing