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Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SD5 PDB entry 7SD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 18% w/v PEG5000 MME
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.136 α = 90 b = 147.136 β = 90 c = 80.108 γ = 90
Symmetry Space Group P 42 21 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-F 2022-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979180 APS 24-ID-C
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 3.12 144.15 100 0.516 0.527 0.104 0.991 6.9 25.6 15333
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 3.12 3.34 100 4.52 4.607 0.887 0.437 26.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 7SD5 3.2 63.55 14187 747 99.39 0.23788 0.23478 0.29747 0.2902 RANDOM 94.464
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] 1.24 1.24 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_3_deg 19.287 r_dihedral_angle_4_deg 16.276 r_long_range_B_refined 10.726 r_long_range_B_other 10.726 r_dihedral_angle_1_deg 8.465 r_scangle_other 4.923 r_mcangle_it 4.436 r_mcangle_other 4.435 r_scbond_it 2.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_3_deg 19.287 r_dihedral_angle_4_deg 16.276 r_long_range_B_refined 10.726 r_long_range_B_other 10.726 r_dihedral_angle_1_deg 8.465 r_scangle_other 4.923 r_mcangle_it 4.436 r_mcangle_other 4.435 r_scbond_it 2.896 r_scbond_other 2.896 r_mcbond_other 2.622 r_mcbond_it 2.621 r_angle_refined_deg 1.539 r_angle_other_deg 1.187 r_chiral_restr 0.236 r_bond_refined_d 0.009 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 4584 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction