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Crystal structure of SARS-CoV-2 Mpro-S144A mutant in complex with 13b-K
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 7.5 298 Ethylene glycols, HEPES, PEG 500 MME, PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.766 α = 90 b = 99.689 β = 90 c = 103.307 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M-F 2022-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.003 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.69 49.31 99.88 0.999 13.71 13.4 78872 31.02
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 1.76 99.7 3.38 0.426
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 1.69 49.31 78872 3819 99.853 0.2 0.1984 0.2087 0.2344 0.2431 38.737
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] -1.874 2.545 -0.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.55 r_dihedral_angle_4_deg 16.321 r_dihedral_angle_3_deg 15.29 r_lrange_it 7.883 r_lrange_other 7.874 r_dihedral_angle_1_deg 7.788 r_scangle_it 5.996 r_scangle_other 5.995 r_mcangle_it 4.825 r_mcangle_other 4.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.55 r_dihedral_angle_4_deg 16.321 r_dihedral_angle_3_deg 15.29 r_lrange_it 7.883 r_lrange_other 7.874 r_dihedral_angle_1_deg 7.788 r_scangle_it 5.996 r_scangle_other 5.995 r_mcangle_it 4.825 r_mcangle_other 4.825 r_scbond_it 4.06 r_scbond_other 4.06 r_dihedral_angle_other_3_deg 3.715 r_mcbond_it 3.462 r_mcbond_other 3.46 r_angle_refined_deg 1.654 r_angle_other_deg 1.378 r_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.182 r_nbd_other 0.177 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.126 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.009 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 4705 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHENIX phasing