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H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
Crystal Properties Matthews coefficient Solvent content 3.92 68.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.598 α = 90 b = 154.598 β = 90 c = 229.312 γ = 90
Symmetry Space Group P 41 2 2
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-F 2020-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.978 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.29 128.187 98 0.094 0.994 4.9 78 40954
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.29 3.35 4.094 0.369
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 FREE R-VALUE 6YLA 3.3 128.187 40954 1939 96.292 0.239 0.2377 0.2416 0.2688 0.2746 144.159
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] -1.97 -1.97 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.684 r_dihedral_angle_3_deg 17.533 r_dihedral_angle_4_deg 14.96 r_dihedral_angle_1_deg 7.668 r_lrange_it 4.952 r_lrange_other 4.951 r_mcangle_it 2.879 r_mcangle_other 2.879 r_scangle_it 2.857 r_scangle_other 2.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.684 r_dihedral_angle_3_deg 17.533 r_dihedral_angle_4_deg 14.96 r_dihedral_angle_1_deg 7.668 r_lrange_it 4.952 r_lrange_other 4.951 r_mcangle_it 2.879 r_mcangle_other 2.879 r_scangle_it 2.857 r_scangle_other 2.857 r_mcbond_other 1.679 r_mcbond_it 1.678 r_scbond_it 1.6 r_scbond_other 1.6 r_angle_refined_deg 1.39 r_angle_other_deg 1.126 r_symmetry_xyhbond_nbd_other 0.32 r_nbd_other 0.237 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.206 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.073 r_ncsr_local_group_2 0.063 r_chiral_restr 0.049 r_ncsr_local_group_1 0.046 r_ncsr_local_group_3 0.042 r_ncsr_local_group_4 0.014 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11686 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling