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BA.2/AZD1061/AZD3152 structure analysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L7E heavy and light chains experimental model PDB 7UB0 RBD experimental model PDB 7ZFF heavy and light chains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.12 M D-glucose, 0.12 M D-mannose, 0.12 M D-galactose, 0.12 M L-fructose, 0.12 M D-xylose, 0.12 M N-acetyl-D-glucosamine, 0.1 M Tris, 0.1 M bicine, pH 8.5, 40% v/v ethylene glycol, 20% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 3.75 67.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.69 α = 90 b = 138 β = 90 c = 188.72 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 CCD RAYONIX MX325HE 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.97741 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.98 94.36 99.7 0.999 9.5 6.7 36925
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 2.98 3.06 0.275
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 7L7E, 7UB0, & 7ZFF 3.3 30.002 27265 1376 99.456 0.282 0.2789 0.2791 0.332 0.3276 120.958
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] -14.157 16.325 -2.168
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.123 r_lrange_other 16.123 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_6_deg 11.856 r_mcangle_it 8.331 r_mcangle_other 8.33 r_scangle_it 7.357 r_scangle_other 7.356 r_dihedral_angle_1_deg 6.177 r_mcbond_it 4.932
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.123 r_lrange_other 16.123 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_6_deg 11.856 r_mcangle_it 8.331 r_mcangle_other 8.33 r_scangle_it 7.357 r_scangle_other 7.356 r_dihedral_angle_1_deg 6.177 r_mcbond_it 4.932 r_mcbond_other 4.932 r_scbond_it 4.202 r_scbond_other 4.202 r_dihedral_angle_2_deg 3.728 r_angle_refined_deg 0.777 r_angle_other_deg 0.286 r_symmetry_nbd_refined 0.222 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.202 r_nbd_other 0.201 r_nbd_refined 0.195 r_nbtor_refined 0.176 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.043 r_chiral_restr 0.035 r_symmetry_xyhbond_nbd_refined 0.02 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8176 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing