6N5A

Crystal structure of an equine H7 hemagglutinin from A/equine/NY/49/73 (H7N7)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BSG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.1 M HEPES, pH 6.5, 2.4 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
4.9274.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.404α = 90
b = 87.404β = 90
c = 524.848γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
13.35099.80.20.050.998.415.719888
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.3610010.370.739.8

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 REPLACEMENTTHROUGHOUT4BSG3.346.241817798699.710.201810.199970.23738RANDOM79.832
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]
-0.21-0.1-0.210.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.45
r_dihedral_angle_3_deg21.185
r_long_range_B_refined18.946
r_long_range_B_other18.945
r_dihedral_angle_4_deg18.866
r_mcangle_it13.403
r_mcangle_other13.401
r_scangle_other12.362
r_dihedral_angle_1_deg9.222
r_mcbond_it8.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.45
r_dihedral_angle_3_deg21.185
r_long_range_B_refined18.946
r_long_range_B_other18.945
r_dihedral_angle_4_deg18.866
r_mcangle_it13.403
r_mcangle_other13.401
r_scangle_other12.362
r_dihedral_angle_1_deg9.222
r_mcbond_it8.642
r_mcbond_other8.642
r_scbond_other7.869
r_scbond_it7.861
r_angle_refined_deg1.951
r_angle_other_deg1.424
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms3838
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing