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Crystal structure of SARS-CoV-2 RBD in complex with human Ab401 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ML9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M Ammonium phosphate monobasic
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.612 α = 90 b = 83.612 β = 90 c = 217.706 γ = 90
Symmetry Space Group P 43 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 2023-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.0358 ALS 2.0.1
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 2.6 45.84 99.7 0.1756 0.19 0.0721 0.995 8.8 6.9 45462 57.35
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 2.6 2.66 97.4 1.973 2.145 0.8342 0.307 0.81 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 45.84 1.34 24680 1998 99.74 0.2219 0.2191 0.2185 0.253 0.2514 62
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 4.7591 f_angle_d 0.4803 f_chiral_restr 0.0413 f_plane_restr 0.0037 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4946 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing