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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 293 25% PEG 3350,
0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.799 α = 90 b = 101.274 β = 90 c = 104.099 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 XE CdTe 16M 2024-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.89 ESRF ID23-1
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 1.197 56.9 99.9 0.1 0.05 0.996 11.3 9.9 223287
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 1.197 1.218 0.728 0.367 0.874 2.3
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 1.2 56.877 212047 11242 99.994 0.15 0.1495 0.1593 0.1876 14.58
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] 1.614 -1.232 -0.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.766 r_lrange_it 10.653 r_dihedral_angle_3_deg 10.524 r_lrange_other 9.164 r_dihedral_angle_1_deg 6.935 r_dihedral_angle_2_deg 5.045 r_scangle_it 4.698 r_scangle_other 4.698 r_mcangle_other 4.102 r_mcangle_it 4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.766 r_lrange_it 10.653 r_dihedral_angle_3_deg 10.524 r_lrange_other 9.164 r_dihedral_angle_1_deg 6.935 r_dihedral_angle_2_deg 5.045 r_scangle_it 4.698 r_scangle_other 4.698 r_mcangle_other 4.102 r_mcangle_it 4.1 r_scbond_it 3.108 r_scbond_other 3.107 r_mcbond_it 2.608 r_mcbond_other 2.602 r_rigid_bond_restr 2.3 r_angle_refined_deg 1.489 r_angle_other_deg 0.537 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.197 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.182 r_nbd_other 0.137 r_ncsr_local_group_1 0.121 r_symmetry_xyhbond_nbd_refined 0.112 r_xyhbond_nbd_refined 0.098 r_metal_ion_refined 0.098 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.079 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4673 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing