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SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5R7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M LiCl, 0.1 M Bis-Tris pH 6.5, 13%(w/v) polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 1.93 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.39 α = 90 b = 52.95 β = 103.51 c = 45.42 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 CCD RIGAKU CCD MSC PAD200sk detector 2021-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54187
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 1.77 26.5 91.63 0.995 19.89 2.7 23834
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 1.77 1.833 0.875
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 (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 1.77 26.5 22662 1190 91.6 0.1696 0.16692 0.1773 0.22256 0.229 RANDOM 15.926
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] 0.55 0.15 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.03 r_dihedral_angle_3_deg 13.177 r_dihedral_angle_4_deg 10.507 r_dihedral_angle_1_deg 7.441 r_long_range_B_refined 5.125 r_long_range_B_other 4.881 r_scangle_other 2.989 r_mcangle_other 2.023 r_mcangle_it 2.022 r_scbond_it 1.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.03 r_dihedral_angle_3_deg 13.177 r_dihedral_angle_4_deg 10.507 r_dihedral_angle_1_deg 7.441 r_long_range_B_refined 5.125 r_long_range_B_other 4.881 r_scangle_other 2.989 r_mcangle_other 2.023 r_mcangle_it 2.022 r_scbond_it 1.963 r_scbond_other 1.963 r_angle_refined_deg 1.648 r_angle_other_deg 1.439 r_mcbond_it 1.29 r_mcbond_other 1.287 r_chiral_restr 0.096 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 2358 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction pointless data scaling PHASER phasing