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Influenza PA-N Endonuclease I38T mutant with compound 2 ((6M)-6-(2-ethylphenyl)-3,4-dihydroxypyridine-2-carboxylic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 32% PEG4000 g/mol, 100 mM Tris, pH 8.35, 220 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.671 α = 90 b = 75.671 β = 90 c = 119.472 γ = 120
Symmetry Space Group P 62 2 2
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 XE 16M 2022-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 1 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 37.84 99.9 0.997 35.7 38.6 14328 55.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.294
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 37.84 1.34 10154 1016 99.98 0.2126 0.2083 0.2516 0.28 68.04
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 21.2427 f_angle_d 0.7774 f_chiral_restr 0.0508 f_plane_restr 0.0084 f_bond_d 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1456 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing