3ZNK

H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IBXPDB ENTRY 2IBX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M HEPES PH 7.0, 0.05 M MGCL2, 28-30 % PEG 550 MME
Crystal Properties
Matthews coefficientSolvent content
4.0470

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.34α = 90
b = 101.23β = 111.31
c = 160.8γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.743.0673.20.17.83.352536361.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2IBX2.7143.0649874266273.150.222880.222140.23651RANDOM52.598
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]
-0.520.4-0.860.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.938
r_dihedral_angle_3_deg17.118
r_dihedral_angle_4_deg16.382
r_dihedral_angle_1_deg5.539
r_angle_refined_deg1.011
r_angle_other_deg0.689
r_scbond_it0.643
r_mcangle_it0.382
r_mcbond_it0.205
r_mcbond_other0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.938
r_dihedral_angle_3_deg17.118
r_dihedral_angle_4_deg16.382
r_dihedral_angle_1_deg5.539
r_angle_refined_deg1.011
r_angle_other_deg0.689
r_scbond_it0.643
r_mcangle_it0.382
r_mcbond_it0.205
r_mcbond_other0.205
r_chiral_restr0.055
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11595
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms321

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing