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Crystal structure of SARS-CoV-2 main protease in complex with RS222C
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 6.7 293 100 mM MES pH 6.7, 11% PEG 4000 and 5% DMSO
150 nL Protein (5 mg/mL), 150 nL Crystallisation condition, 50 nL seed stock (1:250)
Crystal Properties Matthews coefficient Solvent content 2.6 52.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.742 α = 90 b = 99.931 β = 90 c = 104.108 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 16M 2023-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.044 72.093 93.2 0.1988 0.2068 0.0561 0.918 9.71 13.21 31215
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) 2.044 2.23 60.4 1.8226 1.8917 0.5023 0.665 1.61 13.36 1561
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 2.044 72.093 31215 1594 68.674 0.192 0.1902 0.1986 0.2319 0.2368 35.256
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] 0.301 -0.738 0.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.45 r_dihedral_angle_6_deg 14.356 r_dihedral_angle_3_deg 13.717 r_lrange_it 9.453 r_lrange_other 9.443 r_scangle_it 7.919 r_scangle_other 7.918 r_dihedral_angle_1_deg 6.38 r_scbond_it 5.677 r_scbond_other 5.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.45 r_dihedral_angle_6_deg 14.356 r_dihedral_angle_3_deg 13.717 r_lrange_it 9.453 r_lrange_other 9.443 r_scangle_it 7.919 r_scangle_other 7.918 r_dihedral_angle_1_deg 6.38 r_scbond_it 5.677 r_scbond_other 5.675 r_mcangle_other 4.992 r_mcangle_it 4.988 r_mcbond_it 3.602 r_mcbond_other 3.589 r_angle_refined_deg 1.377 r_angle_other_deg 0.418 r_symmetry_nbd_refined 0.262 r_nbd_other 0.239 r_symmetry_xyhbond_nbd_other 0.215 r_symmetry_nbd_other 0.208 r_nbd_refined 0.207 r_metal_ion_refined 0.2 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.143 r_ncsr_local_group_1 0.096 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_other 0.006 r_gen_planes_refined 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4604 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 41
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling REFMAC refinement