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Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW248
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 1.98 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.898 α = 60.63 b = 54.903 β = 79.77 c = 62.261 γ = 88.83
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) 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 1.7 50 85.2 0.083 0.985 23.99 2.8 58337
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.51 0.627 2.36
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 1.7 47.75 49857 2623 90.01 0.1753 0.1732 0.1817 0.2166 0.221 RANDOM 26.328
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] -0.81 0.22 0.35 1.88 0.28 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 16.398 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 7.492 r_angle_refined_deg 1.696 r_angle_other_deg 1.436 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 16.398 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 7.492 r_angle_refined_deg 1.696 r_angle_other_deg 1.436 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4696 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing