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Structure of compound 1 bound to SARS-CoV-2 main protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Internal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Morpheus B3
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.046 α = 90 b = 99.654 β = 90 c = 104.145 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2022-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.276 57.03 99.8 0.136 0.048 0.997 8.2 6 183140
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.276 1.299 98.1 2.77 1.01 0.371 0.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.276 57.03 182872 9101 99.593 0.165 0.164 0.1747 0.1918 0.1976 16.904
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] -0.358 -0.187 0.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.846 r_dihedral_angle_3_deg 10.779 r_lrange_it 10.46 r_lrange_other 8.98 r_dihedral_angle_2_deg 6.968 r_dihedral_angle_1_deg 6.866 r_scangle_it 5.683 r_scangle_other 5.682 r_mcangle_other 4.43 r_mcangle_it 4.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.846 r_dihedral_angle_3_deg 10.779 r_lrange_it 10.46 r_lrange_other 8.98 r_dihedral_angle_2_deg 6.968 r_dihedral_angle_1_deg 6.866 r_scangle_it 5.683 r_scangle_other 5.682 r_mcangle_other 4.43 r_mcangle_it 4.429 r_scbond_it 3.765 r_scbond_other 3.764 r_mcbond_it 2.867 r_mcbond_other 2.856 r_rigid_bond_restr 2.251 r_angle_refined_deg 1.489 r_angle_other_deg 0.532 r_nbd_refined 0.209 r_nbd_other 0.2 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.169 r_ncsr_local_group_1 0.122 r_xyhbond_nbd_refined 0.113 r_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.076 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4696 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing