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The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-4-oxo-4H-pyran-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 8 308 25% PEG4000, 100 mM Tris, pH 8.0, 200 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.84 α = 90 b = 75.84 β = 90 c = 121.3 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 CCD APEX II CCD 2016-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.89 30.33 95.7 0.117 12.5 8.8 4826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3.07 99.8 0.485 2.5 5.4
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 2.89 28.89 4332 473 95.58 0.20684 0.19963 0.2085 0.27586 0.2798 RANDOM 43.918
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] -0.47 -0.23 -0.47 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.87 r_dihedral_angle_4_deg 22.421 r_dihedral_angle_3_deg 19.418 r_long_range_B_other 7.288 r_long_range_B_refined 7.287 r_dihedral_angle_1_deg 6.941 r_scangle_other 4.769 r_mcangle_it 4.653 r_mcangle_other 4.651 r_scbond_other 3.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.87 r_dihedral_angle_4_deg 22.421 r_dihedral_angle_3_deg 19.418 r_long_range_B_other 7.288 r_long_range_B_refined 7.287 r_dihedral_angle_1_deg 6.941 r_scangle_other 4.769 r_mcangle_it 4.653 r_mcangle_other 4.651 r_scbond_other 3.008 r_scbond_it 3.003 r_mcbond_it 2.87 r_mcbond_other 2.858 r_angle_refined_deg 1.277 r_angle_other_deg 0.844 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1496 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing