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The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.1 M Acetate buffer, 0.8 M NaH2PO4 / 1.2 M K2HPO4
Crystal Properties Matthews coefficient Solvent content 3.67 66.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.403 α = 90 b = 82.403 β = 90 c = 134.503 γ = 120
Symmetry Space Group P 32 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 PILATUS3 X 6M 2020-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 48.99 99.1 0.095 0.098 0.025 6.8 13.7 69708
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 1.6 1.63 89.5 0.817 0.871 0.293 0.741 1.71 8.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6W9C 1.6 48.99 66140 3516 98.98 0.1255 0.1234 0.1643 0.1912 RANDOM 28.527
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] -0.07 -0.03 -0.07 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.188 r_dihedral_angle_4_deg 17.253 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_1_deg 6.017 r_rigid_bond_restr 2.469 r_angle_refined_deg 1.433 r_angle_other_deg 1.427 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.188 r_dihedral_angle_4_deg 17.253 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_1_deg 6.017 r_rigid_bond_restr 2.469 r_angle_refined_deg 1.433 r_angle_other_deg 1.427 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2507 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 30
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing