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Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M MES pH 5.8, 15% polyethylene glycol (PEG) 6000, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.245 α = 90 b = 99.143 β = 107.86 c = 58.903 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 EIGER X 16M 2020-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL24XU 1.0 SPring-8 BL24XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.25 56.14 95.08 0.05873 0.0636 10.52 2.68 158113 15.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 1.05 1.249
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6LU7 1.25 56.06 154907 3202 95.13 0.1452 0.1446 0.1769 0.1968 RANDOM 26.307
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] -0.66 -0.97 0.39 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.086 r_dihedral_angle_4_deg 18.118 r_dihedral_angle_3_deg 12.783 r_rigid_bond_restr 9.979 r_dihedral_angle_1_deg 7.123 r_angle_refined_deg 1.955 r_chiral_restr 0.123 r_gen_planes_refined 0.016 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4662 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction DIALS data scaling MOLREP phasing Coot model building