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The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 1-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxy-2-methylpyridin-4(1H)-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AWM PDB entry 4AWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 306 30% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.34 α = 90 b = 75.34 β = 90 c = 120.61 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 PILATUS3 6M 2017-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 44.29 100 0.095 0.1 0.032 19.2 17.5 7520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 0.463 0.487 0.15 5.7 19.4
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 PDB entry 4AWM 2.5 44.29 6950 507 99.49 0.21045 0.2065 0.2153 0.26493 0.2691 RANDOM 48.708
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] -0.29 -0.14 -0.29 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 22.152 r_dihedral_angle_3_deg 16.371 r_long_range_B_refined 9.211 r_long_range_B_other 9.208 r_scangle_other 7.25 r_dihedral_angle_1_deg 6.113 r_mcangle_it 4.928 r_mcangle_other 4.925 r_scbond_it 4.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 22.152 r_dihedral_angle_3_deg 16.371 r_long_range_B_refined 9.211 r_long_range_B_other 9.208 r_scangle_other 7.25 r_dihedral_angle_1_deg 6.113 r_mcangle_it 4.928 r_mcangle_other 4.925 r_scbond_it 4.616 r_scbond_other 4.613 r_mcbond_other 3.316 r_mcbond_it 3.314 r_angle_refined_deg 1.589 r_angle_other_deg 1.059 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1459 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing