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Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor boceprevir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate pH 6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.02 39.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.767 α = 90 b = 53.37 β = 101.833 c = 45.949 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 6M 2020-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 2.4 48.13 99.9 0.093 0.101 0.039 0.999 15.6 6.7 10684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.496 0.663 6.5
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 FREE R-VALUE 6Y2E 2.4 34.44 10684 512 99.85 0.184 0.1801 0.1845 0.2694 0.2642 52.68
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] 1.082 0.593 1.961 -3.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 17.398 r_dihedral_angle_4_deg 15.229 r_lrange_it 8.787 r_lrange_other 8.787 r_dihedral_angle_1_deg 8.379 r_scangle_it 6.353 r_scangle_other 6.351 r_mcangle_it 6.169 r_mcangle_other 6.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 17.398 r_dihedral_angle_4_deg 15.229 r_lrange_it 8.787 r_lrange_other 8.787 r_dihedral_angle_1_deg 8.379 r_scangle_it 6.353 r_scangle_other 6.351 r_mcangle_it 6.169 r_mcangle_other 6.138 r_mcbond_it 4.334 r_mcbond_other 4.309 r_scbond_it 4.218 r_scbond_other 4.217 r_angle_refined_deg 1.927 r_angle_other_deg 1.496 r_symmetry_xyhbond_nbd_refined 0.226 r_nbd_refined 0.219 r_nbd_other 0.199 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.172 r_chiral_restr 0.171 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.038 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_dihedral_angle_other_3_deg 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2319 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOLREP phasing SCALA data scaling