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Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7A91 RBD in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.483 α = 90 b = 177.458 β = 90 c = 209.861 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 EIGER2 X 16M 2023-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.97917 SSRF BL17UM
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 3.1 48.42 98.9 0.176 0.196 0.084 0.993 8 5.2 49491
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 3.1 3.2 98.6 1.348 1.495 0.63 0.45 5.3
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 7A91, AlphaFold 3.1 45.17 47047 2386 98.72 0.22477 0.22183 0.28272 0.2545 RANDOM 85.456
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] 1 1.41 -2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.741 r_dihedral_angle_2_deg 16.106 r_long_range_B_refined 15.769 r_long_range_B_other 15.768 r_scangle_other 13.061 r_dihedral_angle_1_deg 12.286 r_mcangle_it 11.251 r_mcangle_other 11.25 r_scbond_it 8.878 r_scbond_other 8.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.741 r_dihedral_angle_2_deg 16.106 r_long_range_B_refined 15.769 r_long_range_B_other 15.768 r_scangle_other 13.061 r_dihedral_angle_1_deg 12.286 r_mcangle_it 11.251 r_mcangle_other 11.25 r_scbond_it 8.878 r_scbond_other 8.877 r_mcbond_it 7.337 r_mcbond_other 7.337 r_angle_refined_deg 3.014 r_angle_other_deg 1.375 r_chiral_restr 0.2 r_bond_refined_d 0.017 r_gen_planes_refined 0.015 r_bond_other_d 0.006 r_gen_planes_other 0.006 r_dihedral_angle_4_deg 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 12237 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing