☰ Navigation Tabs
Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor MC12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.1M Bis-Tris pH6.5, 18% (v/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.5 α = 90 b = 81.33 β = 97.314 c = 88.864 γ = 90
Symmetry Space Group I 1 2 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 PILATUS3 R 200K-A 2024-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.967 29.19 99.7 0.11 0.15 0.1 0.991 5.4 3.1 25783
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 1.97 2.02 0.549 0.738 0.49 0.768 2.9
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 1.967 24.184 25724 1204 99.451 0.212 0.2099 0.2058 0.25 0.2435 27.898
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] -1.882 0.71 1.485 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.374 r_dihedral_angle_3_deg 16.359 r_dihedral_angle_6_deg 14.117 r_lrange_other 8.805 r_lrange_it 8.798 r_dihedral_angle_1_deg 7.679 r_scangle_it 6.892 r_scangle_other 6.89 r_mcangle_it 5.015 r_mcangle_other 5.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.374 r_dihedral_angle_3_deg 16.359 r_dihedral_angle_6_deg 14.117 r_lrange_other 8.805 r_lrange_it 8.798 r_dihedral_angle_1_deg 7.679 r_scangle_it 6.892 r_scangle_other 6.89 r_mcangle_it 5.015 r_mcangle_other 5.015 r_scbond_it 4.884 r_scbond_other 4.883 r_mcbond_it 3.697 r_mcbond_other 3.681 r_angle_refined_deg 2.607 r_angle_other_deg 0.856 r_nbd_refined 0.232 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.188 r_nbd_other 0.186 r_chiral_restr 0.124 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_nbd_refined 0.097 r_symmetry_nbtor_other 0.096 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing