2RFU

Crystal structure of influenza B virus hemagglutinin in complex with LSTc receptor analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnliganded influenza B virus hemagglutinin

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291100 mM Pipes, 2.5 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.3863.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.369α = 90
b = 98.369β = 90
c = 135.896γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
12.72092.60.05320.9212801970522
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)
12.72.889.90.2972.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUnliganded influenza B virus hemagglutinin2.8201732015990175392.320.296270.294660.31093RANDOM52.168
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]
6.593.36.59-9.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.401
r_dihedral_angle_4_deg21.418
r_dihedral_angle_3_deg20.975
r_dihedral_angle_1_deg7.784
r_scangle_it3.041
r_angle_other_deg2.658
r_scbond_it1.974
r_mcangle_it1.631
r_angle_refined_deg1.519
r_mcbond_it1.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.401
r_dihedral_angle_4_deg21.418
r_dihedral_angle_3_deg20.975
r_dihedral_angle_1_deg7.784
r_scangle_it3.041
r_angle_other_deg2.658
r_scbond_it1.974
r_mcangle_it1.631
r_angle_refined_deg1.519
r_mcbond_it1.364
r_nbd_refined0.245
r_nbd_other0.242
r_symmetry_vdw_other0.236
r_symmetry_vdw_refined0.235
r_xyhbond_nbd_refined0.192
r_nbtor_refined0.189
r_symmetry_hbond_refined0.179
r_mcbond_other0.124
r_nbtor_other0.105
r_chiral_restr0.072
r_xyhbond_nbd_other0.011
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_gen_planes_other0.002
r_bond_other_d0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3864
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms199

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing