7M7W

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JX3PDB entry 7JX3, homology models of S2X259 Fab and S2H97 Fab

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1530% Precipitant Mix 2 (Molecular Dimensions; ethylene glycol, PEG8000), 0.1 M Buffer System 3, pH 8.5 (Molecular Dimensions; Tris (base)/BICINE), 0.12 M Monosaccharides Mix (Molecular Dimensions), 0.02 M sodium chloride, 0.01 M MES, pH 6, 3% v/v Jeffamine ED-2003
Crystal Properties
Matthews coefficientSolvent content
2.9558.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.185α = 90
b = 66.402β = 94.34
c = 237.659γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-03-21MSINGLE 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
12.6563.9498.60.1490.1610.060.99710.96.977307
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)
12.652.798.32.4942.6961.0130.366.8

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, homology models of S2X259 Fab and S2H97 Fab2.6550.0173189377197.950.22360.22120.271RANDOM75.747
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]
1.491.2-1.740.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.664
r_dihedral_angle_3_deg15.912
r_dihedral_angle_4_deg14.671
r_dihedral_angle_1_deg6.69
r_angle_refined_deg0.817
r_chiral_restr0.065
r_gen_planes_refined0.003
r_bond_refined_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16162
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing