☰ Navigation Tabs
The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, at room temperature
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
Crystal Properties Matthews coefficient Solvent content 3.71 66.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.439 α = 90 b = 82.439 β = 90 c = 135.713 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 295 PIXEL DECTRIS PILATUS3 X 6M 2020-05-26 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 2.48 49.23 100 0.167 0.176 0.056 3.7 9.8 19357
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 2.5 2.54 100 1.607 1.707 0.57 0.514 1.4 8.9
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 2.48 49.23 18320 1004 98.97 0.1535 0.1513 0.1568 0.193 0.193 RANDOM 55.079
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] 0.2 0.1 0.2 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.224 r_dihedral_angle_4_deg 25.182 r_dihedral_angle_3_deg 16.406 r_dihedral_angle_1_deg 6.608 r_angle_refined_deg 1.578 r_angle_other_deg 1.316 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.224 r_dihedral_angle_4_deg 25.182 r_dihedral_angle_3_deg 16.406 r_dihedral_angle_1_deg 6.608 r_angle_refined_deg 1.578 r_angle_other_deg 1.316 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2483 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 7
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing