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Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004
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, SITTING DROP 7 277 0.1 M Bis_tris propane, pH 7.0, 2.8 M sodium acetate, 0.1 M glycine, 4 mM ligand
Crystal Properties Matthews coefficient Solvent content 3.27 62.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.02 α = 90 b = 170.02 β = 90 c = 97.588 γ = 90
Symmetry Space Group P 41 21 2
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 2021-01-29 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) 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 2.17 49.06 100 0.143 1 7.1 12.7 75825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.21 100 1.979 0.507 1.27 11.9
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 2.17 49.06 71961 3793 99.93 0.18134 0.17962 0.1842 0.21445 0.213 RANDOM 55.623
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] -0.08 -0.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.836 r_dihedral_angle_4_deg 17.673 r_dihedral_angle_3_deg 15.231 r_dihedral_angle_1_deg 6.267 r_long_range_B_refined 6.116 r_long_range_B_other 6.105 r_scangle_other 4.196 r_mcangle_it 2.878 r_mcangle_other 2.878 r_scbond_it 2.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.836 r_dihedral_angle_4_deg 17.673 r_dihedral_angle_3_deg 15.231 r_dihedral_angle_1_deg 6.267 r_long_range_B_refined 6.116 r_long_range_B_other 6.105 r_scangle_other 4.196 r_mcangle_it 2.878 r_mcangle_other 2.878 r_scbond_it 2.648 r_scbond_other 2.648 r_mcbond_it 1.957 r_mcbond_other 1.955 r_angle_refined_deg 1.61 r_angle_other_deg 1.274 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 7463 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 227
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement HKL-3000 data reduction HKL-3000 phasing