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Crystal structure of SARS coronavirus main protease in complex with an inhibitor Shikonin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.11 60.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.336 α = 90.94 b = 60.62 β = 102.703 c = 68.295 γ = 108.62
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 2020-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
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 2.28 46.03 95 0.046 14.4 3.5 35348 44.1114493017
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 2.28 2.4 0.412
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 NONE 7DQZ 2.28085164536 27.3269337675 1.96354714251 35010 1711 94.1053140876 0.229401915012 0.227151126139 0.2296 0.271979188709 0.2733 59.1759847793
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 3.68708357616 f_angle_d 0.957865513921 f_chiral_restr 0.0511950546766 f_bond_d 0.00748939482694 f_plane_restr 0.00593327725769
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4390 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing