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Structure of SARS-CoV-2 Main Protease bound to Climbazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG 1500
5% DMSO
0.1 M MIB pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.504 α = 90 b = 52.829 β = 102.801 c = 44.663 γ = 90
Symmetry Space Group C 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 DECTRIS PILATUS 6M-F 2020-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 27.43 99.67 0.999 14.61 3.7 43435 17.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.523 0.8781 1.028 0.623
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 6YNQ 1.47 27.43 1.35 43424 1470 99.69 0.1663 0.1654 0.1696 0.1924 0.1921 25.49
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 18.0477 f_angle_d 0.9379 f_chiral_restr 0.0789 f_bond_d 0.007 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction DIALS data reduction XSCALE data scaling PHENIX phasing