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Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 0.05M MgCl2, 0.1M HEPES, pH 7.5, 30% PEG550MME
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.515 α = 90 b = 45.548 β = 96.33 c = 94.737 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 PILATUS 6M-F 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.21 44.4 99.4 0.087 0.04 0.979 18.9 4.7 20441 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.29 99.5 0.217 0.097 4.5
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 2bez 2.21 31.39 19426 1020 98.75 0.2042 0.2019 0.2021 0.24809 0.2483 RANDOM 42.831
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] 5.52 1.44 -1.89 -3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.087 r_dihedral_angle_3_deg 14.299 r_dihedral_angle_4_deg 10.673 r_long_range_B_refined 6.904 r_dihedral_angle_1_deg 4.392 r_scbond_it 3.319 r_mcangle_it 3.075 r_mcbond_it 2.039 r_angle_refined_deg 1.259 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.087 r_dihedral_angle_3_deg 14.299 r_dihedral_angle_4_deg 10.673 r_long_range_B_refined 6.904 r_dihedral_angle_1_deg 4.392 r_scbond_it 3.319 r_mcangle_it 3.075 r_mcbond_it 2.039 r_angle_refined_deg 1.259 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2950 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing