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SARS-CoV-2 main proteinase complex with microbial metabolite leupeptin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG 1500, 0.1 M BIS-TRIS, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.041 α = 90 b = 53.125 β = 101.045 c = 113.635 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 PIXEL DECTRIS EIGER2 XE 16M 2020-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U
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 1.7 50 100 0.063 0.999 29.9 6.8 59085
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 1.7 1.76 0.063 0.999
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 7C6S 1.7 47.96 8.31 59085 2817 99.2 0.2366 0.235 0.2381 0.2602 0.262 19.82
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 12.8053 f_angle_d 0.7964 f_chiral_restr 0.0657 f_bond_d 0.0094 f_plane_restr 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4614 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing