5F9D

Blood group antigen binding adhesin BabA of Helicobacter pylori strain P436 in complex with Lewis b blood group B heptasaccharide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82931 M Sodium acetate, 100 mM Imidazole pH 8.0
Crystal Properties
Matthews coefficientSolvent content
469.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.18α = 90
b = 135.09β = 90
c = 127.33γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.98DiamondI04-1

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
12.5973.1599.50.06715.66.732091
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.592.6699.51.77

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 REPLACEMENTTHROUGHOUT5F7K2.5973.1530496158499.270.196890.194950.23365RANDOM70.459
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]
2.03-0.15-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.693
r_dihedral_angle_4_deg21.209
r_dihedral_angle_3_deg17.314
r_long_range_B_other10.146
r_long_range_B_refined10.145
r_scangle_other8.838
r_mcangle_it6.542
r_mcangle_other6.542
r_dihedral_angle_1_deg6.281
r_scbond_it6.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.693
r_dihedral_angle_4_deg21.209
r_dihedral_angle_3_deg17.314
r_long_range_B_other10.146
r_long_range_B_refined10.145
r_scangle_other8.838
r_mcangle_it6.542
r_mcangle_other6.542
r_dihedral_angle_1_deg6.281
r_scbond_it6.042
r_scbond_other6.04
r_mcbond_other4.458
r_mcbond_it4.457
r_angle_refined_deg1.792
r_angle_other_deg0.877
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3967
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing