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Complex Structure of SARS-CoV-2 3CL Protease with TG-0205221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 14% PEG 1,000, 0.1 M citric acid, pH 3.5.
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.42 α = 90 b = 104.42 β = 90 c = 89.888 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD RAYONIX MX300-HS 2020-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
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 2.05 25 99.9 0.96 39.5 18.2 18754
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 2.05 2.12 0.99
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZU4 2.05 24.17 18166 893 97.217 0.187 0.1843 0.2334 0.2515 30.021
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] -0.105 -0.052 -0.105 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.993 r_dihedral_angle_3_deg 15.346 r_dihedral_angle_4_deg 14.799 r_dihedral_angle_1_deg 7.873 r_lrange_it 6.048 r_lrange_other 5.837 r_scangle_it 2.96 r_scangle_other 2.959 r_dihedral_angle_other_3_deg 2.916 r_mcangle_other 2.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.993 r_dihedral_angle_3_deg 15.346 r_dihedral_angle_4_deg 14.799 r_dihedral_angle_1_deg 7.873 r_lrange_it 6.048 r_lrange_other 5.837 r_scangle_it 2.96 r_scangle_other 2.959 r_dihedral_angle_other_3_deg 2.916 r_mcangle_other 2.553 r_mcangle_it 2.552 r_angle_refined_deg 1.904 r_scbond_it 1.826 r_scbond_other 1.826 r_mcbond_it 1.506 r_mcbond_other 1.485 r_angle_other_deg 1.445 r_nbd_other 0.31 r_symmetry_nbd_refined 0.267 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.172 r_chiral_restr 0.102 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.028 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling MOLREP phasing