☰ Navigation Tabs
Crystal structure of chimeric omicron RBD (strain XBB.1) complexed with human ACE2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 298 100 mM Tris, pH 8.2, 24% PEG6000, 150 mM sodium chloride, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.74 α = 90 b = 116.369 β = 92.81 c = 111.658 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 2023-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 2.706 111.524 85.5 0.152 0.152 0.174 0.085 0.993 5.3 4.1 24963 62.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.706 3.035 0.93 0.93 1.071 0.525 0.549 1.7
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 PDB entry 2AJF 2.71 111.52 1.35 24931 1275 44.99 0.2221 0.2188 0.219 0.2829 0.2832 71.67
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 14.3466 f_angle_d 0.6239 f_chiral_restr 0.0445 f_bond_d 0.0038 f_plane_restr 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12772 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 361
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASES phasing