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SARS-CoV-2 3CL protease with a bound inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.86 α = 90 b = 101.85 β = 90 c = 104.25 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 EIGER X 16M 2023-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.39 72.853 96.3 0.08 1 12.7 6.6 767039
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.497 0.696 0.599 1.7
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 1.39 72.853 116189 5633 79.903 0.177 0.1763 0.1763 0.198 0.1979 16.012
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] -0.005 0.017 -0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.947 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_1_deg 6.921 r_dihedral_angle_2_deg 6.587 r_lrange_it 5.917 r_lrange_other 5.917 r_scangle_it 4.627 r_scangle_other 4.622 r_scbond_it 3.122 r_scbond_other 3.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.947 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_1_deg 6.921 r_dihedral_angle_2_deg 6.587 r_lrange_it 5.917 r_lrange_other 5.917 r_scangle_it 4.627 r_scangle_other 4.622 r_scbond_it 3.122 r_scbond_other 3.119 r_mcangle_other 2.31 r_mcangle_it 2.309 r_angle_refined_deg 1.715 r_mcbond_it 1.626 r_mcbond_other 1.626 r_angle_other_deg 0.578 r_nbd_refined 0.219 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.157 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.132 r_ncsr_local_group_1 0.129 r_symmetry_xyhbond_nbd_refined 0.128 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.083 r_dihedral_angle_other_3_deg 0.022 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4701 Nucleic Acid Atoms Solvent Atoms 604 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing