5F7W

Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group B Lewis b heptasaccharide


X-RAY DIFFRACTION

Starting Model(s)

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

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
3.2261.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.09α = 90
b = 132.44β = 94.93
c = 123.51γ = 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 I040.96863DiamondI04

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
12.8143.299.70.0812.54.639799
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)
12.812.8899.90.7511.84.7

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 REPLACEMENTTHROUGHOUT5F7K2.8143.237751202699.570.172630.17070.20753RANDOM74.223
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]
1.47-0.230.65-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.52
r_dihedral_angle_4_deg21.182
r_dihedral_angle_3_deg17.566
r_long_range_B_refined7.934
r_long_range_B_other7.934
r_dihedral_angle_1_deg6.475
r_scangle_other6.174
r_mcangle_it4.858
r_mcangle_other4.857
r_scbond_it3.962
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.52
r_dihedral_angle_4_deg21.182
r_dihedral_angle_3_deg17.566
r_long_range_B_refined7.934
r_long_range_B_other7.934
r_dihedral_angle_1_deg6.475
r_scangle_other6.174
r_mcangle_it4.858
r_mcangle_other4.857
r_scbond_it3.962
r_scbond_other3.961
r_mcbond_it3.146
r_mcbond_other3.146
r_angle_refined_deg1.622
r_angle_other_deg0.94
r_chiral_restr0.079
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms48
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing