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The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-methyl-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 28% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.51 α = 90 b = 75.51 β = 90 c = 120.16 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 2.25 44.24 100 0.048 0.05 0.015 38.9 19.1 10206
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 2.25 2.32 100 0.532 0.56 0.175 6.4 19
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 2.25 44.24 9651 520 99.96 0.2139 0.21158 0.2212 0.25707 0.2607 RANDOM 48.644
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] -0.19 -0.09 -0.19 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.414 r_dihedral_angle_4_deg 19.346 r_dihedral_angle_3_deg 17.559 r_long_range_B_refined 7.703 r_long_range_B_other 7.683 r_scangle_other 6.294 r_dihedral_angle_1_deg 5.95 r_mcangle_it 5.083 r_mcangle_other 5.081 r_scbond_it 4.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.414 r_dihedral_angle_4_deg 19.346 r_dihedral_angle_3_deg 17.559 r_long_range_B_refined 7.703 r_long_range_B_other 7.683 r_scangle_other 6.294 r_dihedral_angle_1_deg 5.95 r_mcangle_it 5.083 r_mcangle_other 5.081 r_scbond_it 4.225 r_scbond_other 4.222 r_mcbond_it 3.652 r_mcbond_other 3.652 r_angle_refined_deg 1.316 r_angle_other_deg 0.927 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 1487 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing