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Influenza A virus polymerase PA subunit endonuclease domain bound to inhibitor Compound 19a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 0.1 M HEPES, pH 7.5, 1.2 M ammonium sulfate, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.796 α = 90 b = 65.736 β = 115.03 c = 66.164 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 2021-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.476 59.95 96.7 0.026 0.037 0.02 0.998 12.7 3.5 81810
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.476 1.501 95.9 0.362 0.494 0.259 0.858 2.2 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.48 59.95 78000 3810 96.73 0.12485 0.12304 0.16214 0.2037 RANDOM 29.928
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] -0.55 -0.47 0.57 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.479 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 14.88 r_scangle_other 7.57 r_long_range_B_refined 7.397 r_long_range_B_other 7.266 r_rigid_bond_restr 6.979 r_scbond_it 6.642 r_scbond_other 6.621 r_mcangle_it 5.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.479 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 14.88 r_scangle_other 7.57 r_long_range_B_refined 7.397 r_long_range_B_other 7.266 r_rigid_bond_restr 6.979 r_scbond_it 6.642 r_scbond_other 6.621 r_mcangle_it 5.677 r_mcangle_other 5.676 r_dihedral_angle_1_deg 5.607 r_mcbond_it 5.015 r_mcbond_other 5.011 r_angle_refined_deg 1.909 r_angle_other_deg 1.488 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3258 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing