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Crystal structure of SARS-CoV 3CLpro in complex with the non-covalent inhibitor WU-04
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 10% 2-propanal, 0.1 M sodium citrate pH 5.4, 10% PEG 10,000
Crystal Properties Matthews coefficient Solvent content 3.41 63.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.496 α = 90 b = 82.677 β = 103.64 c = 107.454 γ = 90
Symmetry Space Group I 1 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 RIGAKU HyPix-6000HE 2020-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.99 30.76 99.46 0.1236 0.1295 0.03849 0.997 33.16 11 31238 21.85
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 1.99 2.061 99.62 0.4076 0.4344 0.149 0.864 5.12 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1uj1 1.99 30.76 1.34 31087 1477 99.5 0.1993 0.1974 0.1982 0.237 0.2379 25.99
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.4767 f_angle_d 0.6386 f_chiral_restr 0.0434 f_plane_restr 0.0049 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 34
Software Software Software Name Purpose CrysalisPro data collection PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing