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Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FE8 2FE8, 2HD5 experimental model PDB 2HD5 2FE8, 2HD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 295 18% PEG 3000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.464 α = 90 b = 68.309 β = 95.66 c = 68.421 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2012-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.976 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 30 99.6 85347 85006
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 1.4 1.45 99.1 0.394 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2FE8, 2HD5 1.4 30 81098 80733 4248 99.55 0.15686 0.15562 0.1539 0.17983 0.1782 RANDOM 18.546
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] -0.52 0.38 -0.15 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.16 r_sphericity_free 18.564 r_dihedral_angle_4_deg 13.277 r_dihedral_angle_3_deg 11.867 r_sphericity_bonded 8.626 r_dihedral_angle_1_deg 5.291 r_rigid_bond_restr 1.773 r_angle_refined_deg 1.38 r_chiral_restr 0.215 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.16 r_sphericity_free 18.564 r_dihedral_angle_4_deg 13.277 r_dihedral_angle_3_deg 11.867 r_sphericity_bonded 8.626 r_dihedral_angle_1_deg 5.291 r_rigid_bond_restr 1.773 r_angle_refined_deg 1.38 r_chiral_restr 0.215 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3095 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling