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Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-22 Fabs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 containing 0.2 M Lithium sulfate, 0.1 M MES pH 6.0 and 20% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 5.35 77.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.378 α = 90 b = 199.378 β = 90 c = 202.444 γ = 120
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 XE 16M 2021-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
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 3.2 87.32 99.8 0.473 0.063 0.998 9.4 57.5 25724 121.27
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 3.2 3.25 0.549 0.5
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 7NXA 3.2 87.32 1.34 25658 1326 99.67 0.1922 0.1904 0.1913 0.2229 0.2226 131.38
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 11.7535 f_angle_d 0.6012 f_chiral_restr 0.0448 f_plane_restr 0.0053 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4950 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 137
Software Software Software Name Purpose GDA data collection PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing