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Influenza A Virus N9 Neuraminidase complex with NANA (Tern/Australia).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 N9 crystals were grown by hanging-drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA (10-15 mg/ml in water) and potassium phosphate buffer 1.4M KH2PO4:3M K2HPO4 in ratio 8:4, pH 6.6 at 20 degrees celsius. Inhibitor complexes obtained by soaking N9 crystals in a solution of 1.4M potassium phosphate buffer, pH 6.8, containing 5mM of inhibitor for 3 hours at 4 degrees celsius. Soaked in glycerol cryo-buffer.
Crystal Properties Matthews coefficient Solvent content 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.2 α = 90 b = 181.2 β = 90 c = 181.2 γ = 90
Symmetry Space Group I 4 3 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 ADSC QUANTUM 315 2001-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.3 48.47 99.7 0.097 16.7 14 122385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 100 0.335 4.3 10.2
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 7NN9 1.3 48.47 116188 6197 99.68 0.0927 0.09126 0.0976 0.11993 0.1249 RANDOM 13.497
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_sphericity_free 32.728 r_dihedral_angle_1_deg 17.791 r_dihedral_angle_4_deg 17.658 r_sphericity_bonded 12.1 r_dihedral_angle_3_deg 11.999 r_rigid_bond_restr 5.228 r_long_range_B_refined 4.747 r_long_range_B_other 4.747 r_scangle_other 3.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_sphericity_free 32.728 r_dihedral_angle_1_deg 17.791 r_dihedral_angle_4_deg 17.658 r_sphericity_bonded 12.1 r_dihedral_angle_3_deg 11.999 r_rigid_bond_restr 5.228 r_long_range_B_refined 4.747 r_long_range_B_other 4.747 r_scangle_other 3.874 r_scbond_it 3.789 r_scbond_other 3.788 r_angle_refined_deg 2.082 r_mcangle_it 1.319 r_mcangle_other 1.319 r_angle_other_deg 1.189 r_mcbond_it 1.135 r_mcbond_other 1.121 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3067 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing