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Crystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E9S 3E9S,5JZE experimental model PDB 5JZE 3E9S,5JZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 65% (v/v) MPD, 0.1 M Tris [pH 8.0], supplemented with 30% (w/v) Trimethylamine N-oxide dihydrate additive in a 1:5 dilution
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.981 α = 90 b = 98.191 β = 90 c = 106.636 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.44 72.23 99.1 0.099 18 2.4 29922
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.53 0.742
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 3E9S,5JZE 2.44 72.23 28405 1529 98.88 0.19615 0.19211 0.1944 0.26744 0.2578 RANDOM 64.266
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] 0.09 -0.01 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.395 r_dihedral_angle_4_deg 21.28 r_dihedral_angle_3_deg 15.493 r_dihedral_angle_1_deg 6.456 r_long_range_B_refined 6.41 r_long_range_B_other 6.41 r_scangle_other 3.811 r_mcangle_other 2.958 r_mcangle_it 2.957 r_scbond_it 2.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.395 r_dihedral_angle_4_deg 21.28 r_dihedral_angle_3_deg 15.493 r_dihedral_angle_1_deg 6.456 r_long_range_B_refined 6.41 r_long_range_B_other 6.41 r_scangle_other 3.811 r_mcangle_other 2.958 r_mcangle_it 2.957 r_scbond_it 2.476 r_scbond_other 2.476 r_mcbond_it 2.009 r_mcbond_other 2.008 r_angle_refined_deg 1.434 r_angle_other_deg 0.754 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 6226 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing