☰ Navigation Tabs
Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K
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 8.5 298 Bis-Tris, Potassium citrate tribasic monohydrate, PEG 3350, Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.032 α = 90 b = 101.709 β = 90 c = 103.205 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 PILATUS 6M-F 2022-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.003 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 2.13 46.061 99.81 0.998 9.71 7.5 40658 42.05
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 2.15 2.23 99.79 0.587 0.94
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 2.13 46.061 40658 2045 99.782 0.215 0.2117 0.2247 0.2719 0.2781 52.502
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] -3.983 5.592 -1.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.567 r_dihedral_angle_4_deg 17.25 r_dihedral_angle_3_deg 16.321 r_lrange_other 9.576 r_lrange_it 9.571 r_dihedral_angle_1_deg 7.962 r_scangle_it 6.633 r_scangle_other 6.632 r_mcangle_it 6.154 r_mcangle_other 6.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.567 r_dihedral_angle_4_deg 17.25 r_dihedral_angle_3_deg 16.321 r_lrange_other 9.576 r_lrange_it 9.571 r_dihedral_angle_1_deg 7.962 r_scangle_it 6.633 r_scangle_other 6.632 r_mcangle_it 6.154 r_mcangle_other 6.145 r_dihedral_angle_other_3_deg 4.279 r_scbond_it 4.22 r_scbond_other 4.219 r_mcbond_it 3.973 r_mcbond_other 3.962 r_angle_refined_deg 1.504 r_angle_other_deg 1.237 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_other 0.229 r_nbd_refined 0.203 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.124 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.051 r_xyhbond_nbd_other 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 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 4666 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHENIX phasing