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Crystal structure of chimeric omicron RBD (strain BA.2) complexed with chimeric mouse ACE2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VW1 PDB entry 6VW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 100 mM Tris, pH 8.5, 18-22% PEG6000, 100 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.81 56.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.048 α = 90 b = 118.467 β = 93.65 c = 110.845 γ = 90
Symmetry Space Group P 1 21 1
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 X 16M 2022-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.84 80.852 54.5 0.061 0.999 10 3.7 26691 83.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 3.2 0.563 0.757
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 FOURIER SYNTHESIS FREE R-VALUE PDB entry 6VW1 2.84 30.39 1.35 26633 1333 54.47 0.2167 0.2137 0.2139 0.2709 0.2704 97.53
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 12.2059 f_angle_d 0.6033 f_chiral_restr 0.0688 f_plane_restr 0.0043 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12706 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 216
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing