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H11-H4 complex with SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.15 α = 90 b = 73.15 β = 90 c = 131.67 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-F 2020-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 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 1.85 57.151 99.5 0.086 0.028 1 18.2 19.7 35506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 99.5 2.05 0.46 0.7 1.7 20.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6YZ5 1.85 57.151 35472 1808 99.733 0.187 0.185 0.2169 0.2229 48.736
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] 2.091 1.046 2.091 -6.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_other_3_deg 24.12 r_dihedral_angle_1_deg 17.387 r_dihedral_angle_4_deg 16.664 r_dihedral_angle_3_deg 12.462 r_lrange_other 8.808 r_lrange_it 8.797 r_scangle_it 6.874 r_scangle_other 6.777 r_scbond_it 4.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_other_3_deg 24.12 r_dihedral_angle_1_deg 17.387 r_dihedral_angle_4_deg 16.664 r_dihedral_angle_3_deg 12.462 r_lrange_other 8.808 r_lrange_it 8.797 r_scangle_it 6.874 r_scangle_other 6.777 r_scbond_it 4.612 r_scbond_other 4.553 r_mcangle_it 3.896 r_mcangle_other 3.895 r_mcbond_it 3.014 r_mcbond_other 3.006 r_angle_refined_deg 1.682 r_angle_other_deg 1.405 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.189 r_nbd_other 0.183 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.146 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2546 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XSCALE data reduction Aimless data scaling PHASER phasing