2RFT

Crystal structure of influenza B virus hemagglutinin in complex with LSTa 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
3.3863.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.328α = 90
b = 98.328β = 90
c = 135.988γ = 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
12.71389.90.04716.6212801914533
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)
12.72.887.60.2912.1

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 hemagglutinin2.8101690515373171690.940.281750.279840.2987RANDOM47.336
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]
4.192.094.19-6.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.959
r_dihedral_angle_3_deg19.6
r_dihedral_angle_4_deg17.823
r_dihedral_angle_1_deg7.447
r_scangle_it3.191
r_scbond_it1.956
r_mcangle_it1.66
r_angle_refined_deg1.458
r_mcbond_it1.345
r_angle_other_deg0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.959
r_dihedral_angle_3_deg19.6
r_dihedral_angle_4_deg17.823
r_dihedral_angle_1_deg7.447
r_scangle_it3.191
r_scbond_it1.956
r_mcangle_it1.66
r_angle_refined_deg1.458
r_mcbond_it1.345
r_angle_other_deg0.96
r_symmetry_vdw_refined0.283
r_symmetry_hbond_refined0.272
r_nbd_refined0.24
r_xyhbond_nbd_refined0.221
r_nbd_other0.216
r_symmetry_vdw_other0.213
r_nbtor_refined0.183
r_mcbond_other0.133
r_nbtor_other0.096
r_chiral_restr0.074
r_xyhbond_nbd_other0.054
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms222

Software

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