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Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human ACE2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AJF PDB entry 2AJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.95 58.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.13 α = 90 b = 120.179 β = 92.44 c = 113.325 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 S 16M 2022-01-11 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 2.61 113 92.6 0.055 0.999 9.3 4 61585 87.71
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 2.61 2.68 0.689
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 2AJF 2.61 30.11 1.35 36461 1734 54.88 0.1906 0.1884 0.1875 0.235 0.2326 93.77
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 10.451 f_angle_d 0.5572 f_chiral_restr 0.0641 f_plane_restr 0.0033 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12740 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 355
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing