4BSD

Human H7N9 Influenza Virus Haemagglutinin (with Asn-133 Glycosylation) in Complex with Avian Receptor Analogue 3'-SLN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TI8PDB ENTRY 1TI8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1291291 K, 0.1 M PIPES PH 7.0, 2.2 M AMMONIUM SULFATE, 1% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.5565

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.95α = 90
b = 115.95β = 90
c = 295.38γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.459.5699.40.0610.373.9301461
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4998.90.5113.3

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 1TI82.459.5627439146795.270.238870.236820.27691RANDOM60.762
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]
0.240.240.24-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.809
r_dihedral_angle_3_deg16.241
r_dihedral_angle_4_deg14.183
r_dihedral_angle_1_deg5.8
r_scbond_it1.34
r_angle_refined_deg1.032
r_mcangle_it0.907
r_angle_other_deg0.705
r_mcbond_it0.506
r_mcbond_other0.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.809
r_dihedral_angle_3_deg16.241
r_dihedral_angle_4_deg14.183
r_dihedral_angle_1_deg5.8
r_scbond_it1.34
r_angle_refined_deg1.032
r_mcangle_it0.907
r_angle_other_deg0.705
r_mcbond_it0.506
r_mcbond_other0.506
r_chiral_restr0.058
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 Atoms3795
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing