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Crystal structure of SARS-CoV-2 Mpro with compound C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JOY 7JOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Tris pH 8, 15 % PEG 8000, 10 % ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.574 α = 74.95 b = 67.47 β = 80.03 c = 93.099 γ = 66.73
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 R 200K-A 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2 25.64 94.6 0.988 6.62 5.1 87146
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 2.07 82.8 0.79 0.62 4.9
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 7JOY 2 25.64 82308 4381 95.55 0.2433 0.2419 0.2468 0.2711 0.2774 RANDOM 27.499
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] 2.06 -1.15 1.46 -1.37 -0.63 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.029 r_dihedral_angle_4_deg 17.768 r_dihedral_angle_3_deg 16.678 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 1.566 r_angle_other_deg 1.345 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.029 r_dihedral_angle_4_deg 17.768 r_dihedral_angle_3_deg 16.678 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 1.566 r_angle_other_deg 1.345 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9428 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction Aimless data scaling PHASER phasing