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SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M sodium formate, 20% PEG 3350 then soaked with the inhibitor (DMSO) and cryo-protection with glycerol (10%)
Crystal Properties Matthews coefficient Solvent content 2.03 39.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.883 α = 90 b = 53.858 β = 100.269 c = 115.296 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 2023-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
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 2.05 39.088 98.8 0.075 0.088 0.046 0.999 11.2 7.1 33779
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 2.05 2.11 1.226 1.433 0.738 0.716 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 39.088 33764 1739 98.509 0.221 0.2177 0.2811 0.2816 45.715
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] -0.197 0.266 -2.051 2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.07 r_dihedral_angle_3_deg 15.024 r_lrange_other 7.617 r_lrange_it 7.614 r_dihedral_angle_1_deg 6.636 r_scangle_it 5.821 r_scangle_other 5.821 r_mcangle_other 4.913 r_mcangle_it 4.912 r_dihedral_angle_2_deg 4.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.07 r_dihedral_angle_3_deg 15.024 r_lrange_other 7.617 r_lrange_it 7.614 r_dihedral_angle_1_deg 6.636 r_scangle_it 5.821 r_scangle_other 5.821 r_mcangle_other 4.913 r_mcangle_it 4.912 r_dihedral_angle_2_deg 4.244 r_scbond_it 3.833 r_scbond_other 3.828 r_mcbond_it 3.41 r_mcbond_other 3.409 r_angle_refined_deg 1.371 r_angle_other_deg 0.483 r_symmetry_xyhbond_nbd_refined 0.331 r_nbd_refined 0.214 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.189 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.181 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4686 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Aimless data scaling PHASER phasing MxCuBE data collection XDS data reduction