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Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-Butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)b- utan-2-yl)carbamate (tert-butyl -GlnLactam-CO-CO-NH-benzyl)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other HCoV-NL63 main protease
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 25% PEG 1,000, pH 6.0
Crystal Properties Matthews coefficient Solvent content 4.3 71.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.65 α = 90 b = 211.29 β = 90 c = 118.26 γ = 90
Symmetry Space Group C 2 2 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 CCD RAYONIX MX225HE 2014-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 44.28 98.2 0.076 0.038 0.996 11.5 4.4 68423
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 2.35 2.48 97.2 0.458 0.25 0.873 3 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT HCoV-NL63 main protease 2.35 42.89 64886 3526 97.98 0.19205 0.18985 0.23196 0.2286 RANDOM 43.818
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] 2.09 -2.25 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 18.575 r_dihedral_angle_3_deg 15.706 r_long_range_B_other 9.957 r_long_range_B_refined 9.956 r_scangle_other 7.838 r_dihedral_angle_1_deg 7.033 r_mcangle_it 6.283 r_mcangle_other 6.282 r_scbond_it 5.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 18.575 r_dihedral_angle_3_deg 15.706 r_long_range_B_other 9.957 r_long_range_B_refined 9.956 r_scangle_other 7.838 r_dihedral_angle_1_deg 7.033 r_mcangle_it 6.283 r_mcangle_other 6.282 r_scbond_it 5.317 r_scbond_other 5.317 r_mcbond_it 4.319 r_mcbond_other 4.316 r_angle_refined_deg 1.937 r_angle_other_deg 1.24 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6804 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement MOLREP phasing SCALA data scaling