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Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW247
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YB7 PDB entry 6YB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 20% PEG3000, 0.1 M sodium citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 1.99 38.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.19 α = 90 b = 54.512 β = 100.02 c = 45.129 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 PILATUS 6M 2020-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.987 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 50 95.1 0.068 0.081 0.043 8.8 3.4 33926
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 1.6 1.63 93.9 0.5 0.602 0.333 0.684 3.1
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 (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 THROUGHOUT PDB entry 6YB7 1.6 32.15 32253 1672 94.78 0.1759 0.1735 0.1826 0.2207 0.2258 RANDOM 22.964
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] 0.6 -0.65 -0.9 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 20.455 r_dihedral_angle_3_deg 14.473 r_dihedral_angle_1_deg 7.414 r_angle_refined_deg 1.747 r_angle_other_deg 1.486 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 20.455 r_dihedral_angle_3_deg 14.473 r_dihedral_angle_1_deg 7.414 r_angle_refined_deg 1.747 r_angle_other_deg 1.486 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 45
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing