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SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2E12 Fab, S309 Fab, and S304 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JX3 PDB entries 7JX3 and 7K3Q experimental model PDB 7K3Q PDB entries 7JX3 and 7K3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Crystal 1: 0.09 M phosphate/citrate, pH 5.5, 27% v/v PEG Smear Low, 4% v/v polypropylene glycol 400, 0.02 M imidazole, pH 7, Crystal 2: 0.09 M phosphate/citrate, pH 5.5, 27% v/v PEG Smear Low, 0.01 M potassium/sodium phosphate, pH 7, 1% v/v PPGBA 230, 1.5% v/v PPGBA 400
Crystal Properties Matthews coefficient Solvent content 5.37 77.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 245.87 α = 90 b = 245.87 β = 90 c = 237.31 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2020-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00003 ALS 4.2.2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.93 49 100 0.295 0.3 0.056 0.998 13.3 28.9 77621
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) Redundancy Number Unique Reflections (All) 1 2.93 2.99 100 7.868 8.016 1.531 0.381 27.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 7JX3 and 7K3Q 2.95 40 71532 3806 98.95 0.2338 0.2323 0.2624 0.2308 RANDOM 116.456
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] -0.38 -0.38 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.193 r_dihedral_angle_4_deg 18.165 r_dihedral_angle_3_deg 16.945 r_dihedral_angle_1_deg 6.999 r_angle_refined_deg 0.936 r_chiral_restr 0.073 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9101 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing