5F8R

Blood group antigen binding adhesin BabA of Helicobacter pylori strain S831 in complex with blood group H Lewis b hexasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F7K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2 M potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.2462

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.794α = 90
b = 131.914β = 94.88
c = 125.393γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.0332SOLEILPROXIMA 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
12.4448.499.50.09210.15.660611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.442.58971.55.2

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 REPLACEMENTTHROUGHOUT5F7K2.4448.457532304999.390.190660.18910.21914RANDOM66.727
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]
1.090.32-1.180.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.276
r_dihedral_angle_4_deg22.93
r_dihedral_angle_3_deg16.715
r_long_range_B_refined7.175
r_long_range_B_other7.171
r_dihedral_angle_1_deg6.551
r_scangle_other5.535
r_mcangle_it4.077
r_mcangle_other4.077
r_scbond_it3.597
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.276
r_dihedral_angle_4_deg22.93
r_dihedral_angle_3_deg16.715
r_long_range_B_refined7.175
r_long_range_B_other7.171
r_dihedral_angle_1_deg6.551
r_scangle_other5.535
r_mcangle_it4.077
r_mcangle_other4.077
r_scbond_it3.597
r_scbond_other3.597
r_mcbond_it2.696
r_mcbond_other2.695
r_angle_refined_deg1.773
r_angle_other_deg1.055
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms7977
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing