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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W41 experimental model PDB 7BZ5 experimental model PDB 4JHA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 18% PEG Smear Broad
0.08 M MgCl2
0.08 M tri-sodium citrate
0.1 M Bis-Tris pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.177 α = 90 b = 110.018 β = 90 c = 149.392 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2021-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9537 MAX IV BioMAX
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 1.9 47.49 100 0.109 0.114 0.031 0.999 14.8 13.6 73863
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 1.9 1.94 100 2.631 2.731 0.73 0.664 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 47.49 70101 3684 99.98 0.17885 0.1769 0.1893 0.21608 0.2253 RANDOM 43.784
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] -2.75 0.09 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.534 r_dihedral_angle_4_deg 15.046 r_dihedral_angle_3_deg 14.737 r_long_range_B_refined 8.65 r_long_range_B_other 8.649 r_dihedral_angle_1_deg 7.658 r_scangle_other 6.92 r_scbond_it 4.875 r_scbond_other 4.875 r_mcangle_it 4.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.534 r_dihedral_angle_4_deg 15.046 r_dihedral_angle_3_deg 14.737 r_long_range_B_refined 8.65 r_long_range_B_other 8.649 r_dihedral_angle_1_deg 7.658 r_scangle_other 6.92 r_scbond_it 4.875 r_scbond_other 4.875 r_mcangle_it 4.646 r_mcangle_other 4.646 r_mcbond_it 3.568 r_mcbond_other 3.556 r_angle_refined_deg 1.707 r_angle_other_deg 1.383 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4747 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction