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Crystal structure of HCoV-NL63 main protease with PF07304814
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7E6L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 3350, pH5.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.094 α = 90 b = 82.794 β = 109.001 c = 64.423 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 EIGER X 9M 2021-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979137 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 2.32 59.66 93.4 0.054 7.9 3.7 25391 40.8932995056
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 2.32 2.45 0.577
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 7E6L 2.32 37.0239 1.33793583676 25329 3726 88.5111327686 0.208654580782 0.203883248774 0.2646373731 0.2866 44.4087182573
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 5.5343676895 f_angle_d 0.901035927192 f_chiral_restr 0.0551345817814 f_bond_d 0.00718351558435 f_plane_restr 0.00498623400849
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4358 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 76
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing