6HGB

Influenza A virus N6 neuraminidase native structure (Duck/England/56).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293N6 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 coefficientSolvent content
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.2α = 90
b = 73.9β = 90.3
c = 106.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate1999-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.93SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.530.6892.10.0859.53.7241948
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5282.50.1842.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1V0Z1.530.682307831116591.80.140170.139090.16136RANDOM13.965
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]
-0.93-0.042.5-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.688
r_dihedral_angle_1_deg23.7
r_dihedral_angle_4_deg18.32
r_dihedral_angle_3_deg12.718
r_long_range_B_refined5.847
r_long_range_B_other5.847
r_scangle_other3.078
r_scbond_it2.13
r_scbond_other2.13
r_angle_refined_deg1.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.688
r_dihedral_angle_1_deg23.7
r_dihedral_angle_4_deg18.32
r_dihedral_angle_3_deg12.718
r_long_range_B_refined5.847
r_long_range_B_other5.847
r_scangle_other3.078
r_scbond_it2.13
r_scbond_other2.13
r_angle_refined_deg1.706
r_mcangle_it1.301
r_mcangle_other1.301
r_angle_other_deg1.008
r_mcbond_it0.888
r_mcbond_other0.887
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms12036
Nucleic Acid Atoms
Solvent Atoms1587
Heterogen Atoms819

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing