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Crystal structure of HCoV 229E main protease in complex with Oridonin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 6000, 10% DMSO, 15% MPD, 0.1M Tris-HCL, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.82 α = 90 b = 75.43 β = 91.079 c = 77.83 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2024-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979191 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.94 77.82 98.9 0.07 16.7 5.6 45676 20.8318437875
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 0.712
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.94 77.82 1.34757097303 45637 2364 98.8455707169 0.218317941176 0.215937380168 0.2178 0.262432052751 0.2631 48.3212278028
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.6872302936 f_angle_d 0.894228715053 f_chiral_restr 0.056064922048 f_bond_d 0.00729893343617 f_plane_restr 0.00498990311738
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4454 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing