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The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
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 0.2 M Ammonium citrate tribasic pH 7.0, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.411 α = 90 b = 54.27 β = 99.42 c = 114.497 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 RIGAKU HyPix-6000HE 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 112.95 99.5 0.09 0.106 0.055 0.995 8.6 3.5 36330
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 98.9 0.277 0.349 0.209 0.845 2.6
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 6y2e 2 112.95 34366 1920 99.29 0.2077 0.205 0.2568 0.2517 RANDOM 18.554
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_dihedral_angle_3_deg 14.271 r_dihedral_angle_4_deg 12.276 r_dihedral_angle_1_deg 6.312 r_angle_refined_deg 1.576 r_angle_other_deg 0.858 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_dihedral_angle_3_deg 14.271 r_dihedral_angle_4_deg 12.276 r_dihedral_angle_1_deg 6.312 r_angle_refined_deg 1.576 r_angle_other_deg 0.858 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4434 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction CrysalisPro data reduction