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Influenza A virus N6 neuraminidase complex with DANA (Duck/England/56).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 N6 crystals were grown by hanging-drop vapour diffusion against 1:1 20%(w/v) PEG-3350 and 2 microM CaCl2 in 150mM NaCl at 20 degrees celsius, starting with equal volumes of N6 (20mg/ml in saline) and 20% (w/v) PEG 3350 and 2 microM in 1% saline. Microseeding with crystals of native N6 was carried out using a super saturated solution of N6 NA in 20% PEG 3350. Inhibitor complex obtained by soaking N6 crystals in a solution of 20% PEG 3350 in 1% saline (mother liquor) containing 27mM DANA at pH7 for 3 hours at 18 degrees celsius.
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.995 α = 90 b = 75.763 β = 90.5 c = 105.976 γ = 90
Symmetry Space Group P 1 21 1
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 4 1999-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
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 1.65 20.05 91.4 0.092 8.1 2.2 184006
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 1.65 1.68 83.2 0.344 2.4 2.2
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 1V0Z 1.65 20.05 174836 9170 91.25 0.1571 0.15565 0.1671 0.18463 0.1936 RANDOM 15.836
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] 0.13 -0.03 -0.31 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.708 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 12.689 r_dihedral_angle_1_deg 7.913 r_long_range_B_refined 3.577 r_long_range_B_other 3.577 r_angle_refined_deg 1.768 r_scangle_other 1.733 r_scbond_it 1.119 r_scbond_other 1.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.708 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 12.689 r_dihedral_angle_1_deg 7.913 r_long_range_B_refined 3.577 r_long_range_B_other 3.577 r_angle_refined_deg 1.768 r_scangle_other 1.733 r_scbond_it 1.119 r_scbond_other 1.118 r_angle_other_deg 1.065 r_mcangle_it 0.815 r_mcangle_other 0.815 r_mcbond_it 0.534 r_mcbond_other 0.534 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12036 Nucleic Acid Atoms Solvent Atoms 1306 Heterogen Atoms 564
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing