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X-ray crystal structure of the SARS-CoV-2 main protease with Calpain I Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2M sodium citrate, 15% PEG3350, 20mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.481 α = 90 b = 80.729 β = 114.36 c = 51.579 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 2020-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 1 CHESS A1
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 1.76 50 97 0.038 0.905 38.4 3.2 35055 23.88
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 1.76 1.79 72.4 0.295 0.905 3.9 2.4
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 6WTK 1.76 43.25 33044 2000 97.69 0.16125 0.15979 0.171 0.18546 0.1999 RANDOM 33.246
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] 0.02 0.2 0.15 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 14.56 r_dihedral_angle_3_deg 12.148 r_long_range_B_refined 7.759 r_long_range_B_other 7.675 r_dihedral_angle_1_deg 6.895 r_scangle_other 3.683 r_scbond_it 2.608 r_scbond_other 2.6 r_mcangle_it 2.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 14.56 r_dihedral_angle_3_deg 12.148 r_long_range_B_refined 7.759 r_long_range_B_other 7.675 r_dihedral_angle_1_deg 6.895 r_scangle_other 3.683 r_scbond_it 2.608 r_scbond_other 2.6 r_mcangle_it 2.371 r_mcangle_other 2.371 r_angle_refined_deg 1.576 r_mcbond_it 1.567 r_mcbond_other 1.566 r_angle_other_deg 1.472 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data scaling HKL-2000 data reduction PHASER phasing REFMAC refinement