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Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 70mM Citric acid, 30mM Bis-Tris propane pH 3.4, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.51 α = 90 b = 90.531 β = 90 c = 162.463 γ = 90
Symmetry Space Group P 2 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 PILATUS3 6M 2021-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 19.82 99.9 0.073 0.076 0.021 0.999 16.5 12.5 63067
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 99.7 0.983 1.046 0.351 0.849 8.7
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 7FBJ 1.9 19.82 59970 3030 99.8 0.1989 0.1969 0.2037 0.2394 0.2444 RANDOM 50.554
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] 1.31 -4.86 3.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.997 r_dihedral_angle_4_deg 18.518 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 7.987 r_angle_refined_deg 1.906 r_angle_other_deg 1.389 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.997 r_dihedral_angle_4_deg 18.518 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 7.987 r_angle_refined_deg 1.906 r_angle_other_deg 1.389 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4866 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing