5F9A

Blood group antigen binding adhesin BabA of Helicobacter pylori strain P436 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 DROP82931 M Sodium acetate, 100 mM Imidazole pH 8.0
Crystal Properties
Matthews coefficientSolvent content
4.170.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.047α = 90
b = 136.167β = 90
c = 124.634γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

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
12.4451.541000.0958.86.539582
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.442.571001.76.4

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 REPLACEMENTTHROUGHOUT5F7K2.4451.5437277199699.260.20730.20480.25744RANDOM57.443
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]
0.270.9-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.294
r_dihedral_angle_4_deg19.705
r_dihedral_angle_3_deg16.28
r_long_range_B_refined7.34
r_long_range_B_other7.339
r_dihedral_angle_1_deg6.732
r_scangle_other5.997
r_mcangle_it4.301
r_mcangle_other4.3
r_scbond_it3.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.294
r_dihedral_angle_4_deg19.705
r_dihedral_angle_3_deg16.28
r_long_range_B_refined7.34
r_long_range_B_other7.339
r_dihedral_angle_1_deg6.732
r_scangle_other5.997
r_mcangle_it4.301
r_mcangle_other4.3
r_scbond_it3.975
r_scbond_other3.975
r_mcbond_it2.881
r_mcbond_other2.879
r_angle_refined_deg1.877
r_angle_other_deg0.988
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms3966
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing