☰ Navigation Tabs
SARS-COV2 Main Protease in complex with inhibitor MG78
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 MMT, PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.52 α = 90 b = 64.04 β = 90 c = 105.38 γ = 90
Symmetry Space Group P 21 21 2
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 2021-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.807 40.69 86.101 0.9 3.57 6 29378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.807 1.854 0.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6y2e 1.807 40.688 24983 1248 86.101 0.238 0.2345 0.2432 0.3002 0.3106 49.403
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] -1.553 -0.715 2.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 20.624 r_dihedral_angle_3_deg 18.07 r_dihedral_angle_other_3_deg 16.223 r_lrange_it 8.145 r_lrange_other 8.118 r_dihedral_angle_1_deg 7.915 r_scangle_it 5.926 r_scangle_other 5.924 r_mcangle_it 5.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 20.624 r_dihedral_angle_3_deg 18.07 r_dihedral_angle_other_3_deg 16.223 r_lrange_it 8.145 r_lrange_other 8.118 r_dihedral_angle_1_deg 7.915 r_scangle_it 5.926 r_scangle_other 5.924 r_mcangle_it 5.419 r_mcangle_other 5.417 r_scbond_it 3.826 r_scbond_other 3.824 r_mcbond_other 3.688 r_mcbond_it 3.686 r_angle_refined_deg 1.52 r_angle_other_deg 1.23 r_symmetry_xyhbond_nbd_refined 0.306 r_nbd_other 0.212 r_nbd_refined 0.21 r_symmetry_nbd_other 0.18 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.152 r_metal_ion_refined 0.08 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_bond_other_d 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing