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Crystal structure of SARS-CoV-2 main protease in complex with RAY1216
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000. Protein concentration 10mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.829 α = 80.03 b = 60.935 β = 68.34 c = 64.037 γ = 70.67
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 PILATUS3 6M 2022-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 59.42 97.5 0.067 9.9 3.5 48627
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.504
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.02 57.47 45281 2275 97.46 0.18839 0.18623 0.1966 0.23118 0.2462 RANDOM 36.078
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] 3.45 2.11 1.04 -1.55 2.61 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.474 r_dihedral_angle_4_deg 17.796 r_dihedral_angle_3_deg 14.395 r_rigid_bond_restr 7.633 r_dihedral_angle_1_deg 7.476 r_long_range_B_refined 4.882 r_long_range_B_other 4.882 r_scangle_other 3.528 r_mcangle_other 3.213 r_mcangle_it 3.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.474 r_dihedral_angle_4_deg 17.796 r_dihedral_angle_3_deg 14.395 r_rigid_bond_restr 7.633 r_dihedral_angle_1_deg 7.476 r_long_range_B_refined 4.882 r_long_range_B_other 4.882 r_scangle_other 3.528 r_mcangle_other 3.213 r_mcangle_it 3.204 r_scbond_it 2.704 r_scbond_other 2.687 r_mcbond_it 2.456 r_mcbond_other 2.442 r_angle_refined_deg 1.479 r_angle_other_deg 1.267 r_chiral_restr 0.091 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4642 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 90
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement