5F7Y

Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group A type-1 hexasaccharide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2M sodium nitrate, 0.1M Bis Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1961.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.87α = 90
b = 131.71β = 94.69
c = 123.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96863DiamondI24

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
12.4434.999.70.09510.65.660096
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)
12.442.599.70.7862.25.7

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 REPLACEMENTTHROUGHOUT5F7K2.4434.957059301299.510.177250.175740.20505RANDOM58.312
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]
0.89-0.27-0.39-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg20.599
r_dihedral_angle_3_deg17.66
r_long_range_B_refined8.011
r_long_range_B_other8.003
r_scangle_other6.485
r_dihedral_angle_1_deg6.285
r_mcangle_it4.408
r_mcangle_other4.408
r_scbond_it4.192
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg20.599
r_dihedral_angle_3_deg17.66
r_long_range_B_refined8.011
r_long_range_B_other8.003
r_scangle_other6.485
r_dihedral_angle_1_deg6.285
r_mcangle_it4.408
r_mcangle_other4.408
r_scbond_it4.192
r_scbond_other4.191
r_mcbond_it2.916
r_mcbond_other2.916
r_angle_refined_deg1.741
r_angle_other_deg1.062
r_chiral_restr0.103
r_bond_refined_d0.017
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 Atoms7970
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing