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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13699
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.07 M Bis-Tris (pH 8.0), 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.732 α = 90 b = 52.847 β = 102.56 c = 45.427 γ = 90
Symmetry Space Group C 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 EIGER2 XE 9M 2024-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 1.0 NSLS-II 19-ID
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 2.46 50 99 0.976 14.59 6.9 9510
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 2.46 2.5 99.8 0.883 2.03 6.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.47 47.76 9025 484 98.75 0.20818 0.20547 0.2125 0.26161 0.2747 RANDOM 46.025
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] 4.43 -0.17 -1.67 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.942 r_dihedral_angle_1_deg 6.85 r_long_range_B_refined 5.541 r_long_range_B_other 5.535 r_dihedral_angle_2_deg 4.441 r_scangle_other 3.535 r_mcangle_it 3.385 r_mcangle_other 3.384 r_scbond_it 2.163 r_scbond_other 2.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.942 r_dihedral_angle_1_deg 6.85 r_long_range_B_refined 5.541 r_long_range_B_other 5.535 r_dihedral_angle_2_deg 4.441 r_scangle_other 3.535 r_mcangle_it 3.385 r_mcangle_other 3.384 r_scbond_it 2.163 r_scbond_other 2.162 r_mcbond_it 2.059 r_mcbond_other 2.055 r_angle_refined_deg 1.075 r_angle_other_deg 0.393 r_chiral_restr 0.054 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing