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SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium acetate trihydrate pH 4.5 and 30% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 3.2 61.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.574 α = 90 b = 205.147 β = 90 c = 123.052 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER2 XE 16M 2022-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.18 67 100 0.728 0.207 0.877 2.5 13.4 8472 150.89
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 4.18 4.25 0.34 0.4
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 7qnw 4.18 61.53 1.33 8184 415 96.68 0.3702 0.3695 0.3637 0.3853 0.3869 195.6
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 12.7122 f_angle_d 1.1303 f_chiral_restr 0.0806 f_plane_restr 0.0082 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5694 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose GDA data collection PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing