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Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M CHES (pH 9.5), 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.76 α = 90 b = 74.76 β = 90 c = 100.07 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 6M 2023-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.72 50 99.9 0.999 16.09 13 34940
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 1.72 1.82 0.702
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2 39.622 22387 1111 99.893 0.225 0.223 0.2257 0.2538 0.2547 65.885
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] 2.838 1.419 2.838 -9.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.127 r_dihedral_angle_6_deg 14.776 r_lrange_it 10.858 r_lrange_other 10.848 r_scangle_it 8.609 r_scangle_other 8.606 r_mcangle_it 7.813 r_mcangle_other 7.809 r_dihedral_angle_1_deg 7.284 r_dihedral_angle_2_deg 6.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.127 r_dihedral_angle_6_deg 14.776 r_lrange_it 10.858 r_lrange_other 10.848 r_scangle_it 8.609 r_scangle_other 8.606 r_mcangle_it 7.813 r_mcangle_other 7.809 r_dihedral_angle_1_deg 7.284 r_dihedral_angle_2_deg 6.672 r_scbond_it 6.099 r_scbond_other 6.082 r_mcbond_it 5.734 r_mcbond_other 5.732 r_angle_refined_deg 1.346 r_angle_other_deg 0.769 r_nbd_refined 0.231 r_symmetry_nbd_other 0.216 r_nbtor_refined 0.193 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.064 r_symmetry_nbd_refined 0.061 r_metal_ion_refined 0.041 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1889 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing