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SARS-COV2 Main Protease in complex with inhibitor MG-131
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 9 293 0.1 M MMT, pH 9.0 plus 25% w/v polyethylenglycol 1500
Crystal Properties Matthews coefficient Solvent content 1.94 36.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.716 α = 90 b = 51.667 β = 103.335 c = 45.451 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 EIGER X 16M 2021-12-16 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) 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 2.52 46.81 99 0.04 0.999 16.2 3.5 49867
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.62 0.996
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 2.52 46.81 8752 420 98.781 0.208 0.2035 0.2091 0.2898 0.2868 44.003
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] 1.881 -1.283 0.932 -1.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.076 r_dihedral_angle_4_deg 22.426 r_dihedral_angle_3_deg 19.084 r_dihedral_angle_1_deg 9.324 r_lrange_it 7.922 r_lrange_other 7.921 r_dihedral_angle_other_3_deg 7.442 r_scangle_it 5.183 r_scangle_other 5.182 r_mcangle_it 4.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.076 r_dihedral_angle_4_deg 22.426 r_dihedral_angle_3_deg 19.084 r_dihedral_angle_1_deg 9.324 r_lrange_it 7.922 r_lrange_other 7.921 r_dihedral_angle_other_3_deg 7.442 r_scangle_it 5.183 r_scangle_other 5.182 r_mcangle_it 4.981 r_mcangle_other 4.979 r_scbond_it 3.171 r_scbond_other 3.17 r_mcbond_other 3.151 r_mcbond_it 3.15 r_angle_refined_deg 1.592 r_angle_other_deg 1.185 r_symmetry_xyhbond_nbd_refined 0.256 r_chiral_restr 0.252 r_nbd_refined 0.225 r_nbd_other 0.221 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.15 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing