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SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JX3 PDB entry 7JX3 and homology model of S2X35 Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.85 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 coefficient Solvent content 3.56 65.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.267 α = 90 b = 239.372 β = 90 c = 129.806 γ = 90
Symmetry Space Group C 2 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 PIXEL DECTRIS PILATUS 6M 2021-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.83 39.52 99.6 0.085 0.092 0.035 0.999 16.2 6.7 144449
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 1.83 1.86 99.5 2.96 3.199 1.202 0.306 7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 7JX3 and homology model of S2X35 Fab 1.83 38.91 135667 7049 98.28 0.2123 0.2113 0.2175 0.2316 0.2375 RANDOM 37.283
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.757 r_dihedral_angle_4_deg 16.847 r_dihedral_angle_3_deg 12.067 r_dihedral_angle_1_deg 7.34 r_angle_refined_deg 1.259 r_angle_other_deg 1.154 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.757 r_dihedral_angle_4_deg 16.847 r_dihedral_angle_3_deg 12.067 r_dihedral_angle_1_deg 7.34 r_angle_refined_deg 1.259 r_angle_other_deg 1.154 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8160 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing