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Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EAM 7EAM, 7CHB, 6XDG experimental model PDB 7CHB 7EAM, 7CHB, 6XDG experimental model PDB 6XDG 7EAM, 7CHB, 6XDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.25 M ammonium sulfate, 22.5% PEG3350, 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.265 α = 90 b = 118.195 β = 90 c = 196.293 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 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 46.71 99.6 0.982 4.1 5 74372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.4 98.1 0.685 1 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7EAM, 7CHB, 6XDG 2.35 46.71 1.33 74092 3688 99.18 0.2307 0.2282 0.2278 0.2785 0.277
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.725 f_angle_d 1.025 f_chiral_restr 0.061 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9661 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing MOLREP phasing