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Structure of 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 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.78 α = 90 b = 99.41 β = 90 c = 103.98 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 2022-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.624 71.8 91.7 0.062 1 13 13.4 67317
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 1.624 1.759 0.582 0.341 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.624 56.846 67317 3504 75.392 0.194 0.1919 0.2256 0.2148 21.442
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 -0.01 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.795 r_dihedral_angle_3_deg 15.363 r_dihedral_angle_2_deg 7.257 r_dihedral_angle_1_deg 7.255 r_lrange_it 7.229 r_lrange_other 7.102 r_scangle_it 5.267 r_scangle_other 5.266 r_scbond_it 3.364 r_scbond_other 3.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.795 r_dihedral_angle_3_deg 15.363 r_dihedral_angle_2_deg 7.257 r_dihedral_angle_1_deg 7.255 r_lrange_it 7.229 r_lrange_other 7.102 r_scangle_it 5.267 r_scangle_other 5.266 r_scbond_it 3.364 r_scbond_other 3.363 r_mcangle_it 3.173 r_mcangle_other 3.173 r_mcbond_it 2.145 r_mcbond_other 2.138 r_angle_refined_deg 1.505 r_angle_other_deg 0.518 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_other 0.206 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.179 r_metal_ion_refined 0.17 r_ncsr_local_group_1 0.116 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing