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Influenza A virus N6 neuraminidase native structure (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.
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.2 α = 90 b = 73.9 β = 90.3 c = 106.4 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 IMAGE PLATE MAR scanner 345 mm plate 1999-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.93 SSRL BL9-1
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 1.5 30.68 92.1 0.085 9.5 3.7 241948
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 1.5 1.52 82.5 0.184 2.7
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 1.5 30.68 230783 11165 91.8 0.14017 0.13909 0.1408 0.16136 0.1628 RANDOM 13.965
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] -0.93 -0.04 2.5 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.688 r_dihedral_angle_1_deg 23.7 r_dihedral_angle_4_deg 18.32 r_dihedral_angle_3_deg 12.718 r_long_range_B_refined 5.847 r_long_range_B_other 5.847 r_scangle_other 3.078 r_scbond_it 2.13 r_scbond_other 2.13 r_angle_refined_deg 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.688 r_dihedral_angle_1_deg 23.7 r_dihedral_angle_4_deg 18.32 r_dihedral_angle_3_deg 12.718 r_long_range_B_refined 5.847 r_long_range_B_other 5.847 r_scangle_other 3.078 r_scbond_it 2.13 r_scbond_other 2.13 r_angle_refined_deg 1.706 r_mcangle_it 1.301 r_mcangle_other 1.301 r_angle_other_deg 1.008 r_mcbond_it 0.888 r_mcbond_other 0.887 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 1587 Heterogen Atoms 819
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing