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Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 8 mM Nickel chloride
80 mM TRIS (pH 8.5)
16% PEG-MME 2,000
20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.26 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.027 α = 90 b = 63.362 β = 90.4 c = 102.831 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 PILATUS3 S 6M 2022-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.6 47.1 99.5 0.059 0.999 18.3 6.8 79374
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 1.6 1.63 98.6 0.883 0.815 2.2 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 6Y2E 1.6 47.07 76114 3238 99.39 0.1746 0.1732 0.1827 0.2064 0.2115 RANDOM 22.404
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] -0.53 0.54 1.43 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.242 r_dihedral_angle_4_deg 19.303 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 7.313 r_angle_refined_deg 1.553 r_angle_other_deg 1.439 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.242 r_dihedral_angle_4_deg 19.303 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 7.313 r_angle_refined_deg 1.553 r_angle_other_deg 1.439 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4736 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing