7R6W

SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JX3PDB entry 7JX3 and homology model of S2X35 Fab

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151.85 M ammonium sulfate, 0.1 M Tris, pH 8.17, 0.8% w/v polyvinyl alcohol, 1% v/v 1-propanol, 0.01 M HEPES, pH 7
Crystal Properties
Matthews coefficientSolvent content
3.5665.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.267α = 90
b = 239.372β = 90
c = 129.806γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.8339.5299.60.0850.0920.0350.99916.26.7144449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.8699.52.963.1991.2020.3067

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 7JX3 and homology model of S2X35 Fab1.8338.91135667704998.280.21230.21130.2316RANDOM37.283
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]
1.59-0.13-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.757
r_dihedral_angle_4_deg16.847
r_dihedral_angle_3_deg12.067
r_dihedral_angle_1_deg7.34
r_angle_refined_deg1.259
r_angle_other_deg1.154
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.757
r_dihedral_angle_4_deg16.847
r_dihedral_angle_3_deg12.067
r_dihedral_angle_1_deg7.34
r_angle_refined_deg1.259
r_angle_other_deg1.154
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8160
Nucleic Acid Atoms
Solvent Atoms584
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing