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The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-(2-methyl-4-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)phenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid
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 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.164 α = 90 b = 75.164 β = 90 c = 120.628 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 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 ALS 5.0.1
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 2.35 44.28 99.9 0.034 0.035 0.01 62.6 23.3 8894
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 2.35 2.44 99.6 0.456 0.475 0.13 7.5 24.1
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 2.35 44.28 8198 672 99.72 0.20041 0.19541 0.2064 0.26027 0.2625 RANDOM 53.646
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] -0.59 -0.29 -0.59 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.397 r_dihedral_angle_4_deg 21.214 r_dihedral_angle_3_deg 17.195 r_long_range_B_other 8.388 r_long_range_B_refined 8.382 r_scangle_other 7.139 r_dihedral_angle_1_deg 5.97 r_mcangle_it 5.195 r_mcangle_other 5.192 r_scbond_it 4.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.397 r_dihedral_angle_4_deg 21.214 r_dihedral_angle_3_deg 17.195 r_long_range_B_other 8.388 r_long_range_B_refined 8.382 r_scangle_other 7.139 r_dihedral_angle_1_deg 5.97 r_mcangle_it 5.195 r_mcangle_other 5.192 r_scbond_it 4.894 r_scbond_other 4.887 r_mcbond_it 3.672 r_mcbond_other 3.665 r_angle_refined_deg 1.348 r_angle_other_deg 0.923 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1468 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing