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The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 0.1 M acetate buffer, 0.8 NaH2PO4/1.2 M K2HPO4, seeds from PLprotease C111S mutant crystals
Crystal Properties Matthews coefficient Solvent content 3.63 66.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.986 α = 90 b = 81.986 β = 90 c = 134.345 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 2020-05-12 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 1.79 48.84 100 0.137 0.142 0.037 6.6 14.2 49598
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 1.79 1.83 100 1.781 1.858 0.523 0.632 1.72 12.4
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 6WRH 1.79 48.84 47056 2498 99.79 0.1607 0.16 0.1684 0.1741 0.1801 RANDOM 36.074
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] 0.18 0.09 0.18 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.303 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 13.659 r_dihedral_angle_1_deg 5.885 r_angle_refined_deg 1.492 r_angle_other_deg 1.421 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.303 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 13.659 r_dihedral_angle_1_deg 5.885 r_angle_refined_deg 1.492 r_angle_other_deg 1.421 r_chiral_restr 0.07 r_bond_refined_d 0.01 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 2502 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 25
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing