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The crystal structure of COVID-19 main protease in complex with GC376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M Lithium chloride, 0.1M Hepes pH 7, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.03 39.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.303 α = 90 b = 53.874 β = 101.576 c = 45.233 γ = 90
Symmetry Space Group C 1 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 PILATUS3 S 6M 2020-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.35 48.57 99.2 0.065 0.065 0.036 0.998 9.7 3 11269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 0.347 0.418 0.23 0.889
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 NONE 1q2w 2.35 44.352 11226 563 98.742 0.215 0.2115 0.2166 0.2728 0.2797 40.478
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] -0.013 -0.013 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_4_deg 15.332 r_dihedral_angle_3_deg 13.32 r_dihedral_angle_1_deg 6.949 r_dihedral_angle_other_3_deg 5.499 r_lrange_it 4.984 r_lrange_other 4.984 r_mcangle_it 2.895 r_mcangle_other 2.892 r_scangle_other 2.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_4_deg 15.332 r_dihedral_angle_3_deg 13.32 r_dihedral_angle_1_deg 6.949 r_dihedral_angle_other_3_deg 5.499 r_lrange_it 4.984 r_lrange_other 4.984 r_mcangle_it 2.895 r_mcangle_other 2.892 r_scangle_other 2.844 r_scangle_it 2.624 r_angle_other_deg 2.391 r_mcbond_it 1.715 r_mcbond_other 1.709 r_scbond_it 1.568 r_scbond_other 1.567 r_angle_refined_deg 1.247 r_symmetry_nbd_refined 0.217 r_symmetry_nbd_other 0.209 r_nbd_refined 0.191 r_nbd_other 0.191 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_other 0.071 r_symmetry_nbtor_other 0.062 r_chiral_restr 0.046 r_bond_other_d 0.036 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2323 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing