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Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 15% PEG 4000
150 mM ammonium sulfate
0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.056 α = 90 b = 111.259 β = 90 c = 142.948 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 PILATUS 6M 2021-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.04 50 98 0.141 0.073 0.978 11.6 4 54854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.08 92.1 0.637 0.425 0.567 1.65 2.6
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 7JMP 2.05 35.9 1.37 53446 2710 95.15 0.1673 0.1657 0.1666 0.1979 0.1992
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 20.147 f_angle_d 0.98 f_chiral_restr 0.062 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4807 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing