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Influenza Virus N9 Neuraminidase A complex with Zanamivir molecule (Tern).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8E
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 18 degrees celsius. Soaked in glycerol cryo-buffer.
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.935 α = 90 b = 180.935 β = 90 c = 180.935 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 2001-12-12 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) Rrim 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 1.29 42.68 99.9 0.093 16.3 10 122689 12.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.4 99.5 0.706 2.3 6.3
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 1F8E 1.3 42.68 116245 6157 99.87 0.09831 0.09691 0.1002 0.1246 0.1269 RANDOM 15.039
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_sphericity_free 37.992 r_dihedral_angle_2_deg 32.275 r_dihedral_angle_1_deg 20.182 r_dihedral_angle_4_deg 19.062 r_sphericity_bonded 12.66 r_dihedral_angle_3_deg 11.788 r_rigid_bond_restr 6.455 r_long_range_B_refined 5.515 r_long_range_B_other 5.515 r_scbond_it 5.06
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.992 r_dihedral_angle_2_deg 32.275 r_dihedral_angle_1_deg 20.182 r_dihedral_angle_4_deg 19.062 r_sphericity_bonded 12.66 r_dihedral_angle_3_deg 11.788 r_rigid_bond_restr 6.455 r_long_range_B_refined 5.515 r_long_range_B_other 5.515 r_scbond_it 5.06 r_scbond_other 5.058 r_scangle_other 4.129 r_angle_refined_deg 1.954 r_mcangle_other 1.485 r_mcangle_it 1.484 r_mcbond_it 1.245 r_mcbond_other 1.237 r_angle_other_deg 1.158 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3067 Nucleic Acid Atoms Solvent Atoms 691 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing