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Crystal structure of SARS-CoV-2 Mpro with compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 (NH4)2SO4: 1.6 M ; Dioxane: 10 %v/v ; MES: 0.1 M pH: 6.50
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.605 α = 90 b = 106.61 β = 103.043 c = 55.375 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2023-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9537 SLS X10SA
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 1.721 53.946 88.2 0.1393 0.1542 0.0652 0.985 5.24 4.98 43129
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) 1.721 1.846 52.7 0.94 1.0352 0.4297 0.673 1.38 5.51 2156
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.849 53.946 42493 2155 90.632 0.194 0.192 0.2363 0.273 23.047
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] -0.386 0.321 -0.667 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 34.679 r_dihedral_angle_2_deg 34.014 r_dihedral_angle_4_deg 14.538 r_dihedral_angle_3_deg 12.4 r_dihedral_angle_6_deg 12.271 r_dihedral_angle_1_deg 7.075 r_lrange_it 4.112 r_lrange_other 3.964 r_mcangle_it 1.817 r_mcangle_other 1.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 34.679 r_dihedral_angle_2_deg 34.014 r_dihedral_angle_4_deg 14.538 r_dihedral_angle_3_deg 12.4 r_dihedral_angle_6_deg 12.271 r_dihedral_angle_1_deg 7.075 r_lrange_it 4.112 r_lrange_other 3.964 r_mcangle_it 1.817 r_mcangle_other 1.817 r_scangle_it 1.778 r_scangle_other 1.778 r_angle_refined_deg 1.37 r_angle_other_deg 1.166 r_scbond_it 1.096 r_scbond_other 1.096 r_mcbond_it 1.062 r_mcbond_other 1.057 r_symmetry_xyhbond_nbd_refined 0.17 r_nbd_refined 0.161 r_nbtor_refined 0.151 r_symmetry_nbd_other 0.149 r_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.126 r_nbd_other 0.118 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.06 r_ncsr_local_group_1 0.033 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4734 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 145
Software Software Software Name Purpose autoPROC data processing autoPROC data processing Aimless data scaling autoPROC data processing REFMAC refinement autoPROC data reduction PHASER phasing