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Crystal structure of canine coronavirus main protease in complex with GC376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.0, 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.975 α = 90 b = 125.749 β = 97.47 c = 160.418 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 CCD RAYONIX MX300-HS 2020-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.75 30 99.3 0.062 0.036 20.39 3.7 79392
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 99.7 0.386 0.234 0.914
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 (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 4F49 2.75 27.82 73326 3926 96.36 0.21356 0.21254 0.215 0.23276 0.2347 RANDOM 50.376
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] -0.06 -0.17 0.07 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_3_deg 19.04 r_dihedral_angle_4_deg 16.939 r_long_range_B_other 9.618 r_long_range_B_refined 9.613 r_dihedral_angle_1_deg 8.561 r_mcangle_it 6.668 r_mcangle_other 6.667 r_scangle_other 6.216 r_mcbond_it 4.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_3_deg 19.04 r_dihedral_angle_4_deg 16.939 r_long_range_B_other 9.618 r_long_range_B_refined 9.613 r_dihedral_angle_1_deg 8.561 r_mcangle_it 6.668 r_mcangle_other 6.667 r_scangle_other 6.216 r_mcbond_it 4.198 r_mcbond_other 4.198 r_scbond_other 3.842 r_scbond_it 3.84 r_angle_other_deg 2.372 r_angle_refined_deg 1.319 r_chiral_restr 0.05 r_bond_other_d 0.036 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 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 18224 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing