5F7N

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


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
3.261.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.85α = 90
b = 131.95β = 94.81
c = 123.81γ = 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
12.2833.298.60.079125.672982
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)
12.282.3497.90.7432.25.6

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 REPLACEMENTTHROUGHOUT5F7K2.2833.269304365198.380.172140.170790.19712RANDOM57.67
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]
1.120.41-1.340.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.673
r_dihedral_angle_4_deg22.173
r_dihedral_angle_3_deg16.374
r_long_range_B_refined7.894
r_long_range_B_other7.891
r_dihedral_angle_1_deg6.9
r_scangle_other6.266
r_scbond_it4.182
r_scbond_other4.182
r_mcangle_it3.999
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.673
r_dihedral_angle_4_deg22.173
r_dihedral_angle_3_deg16.374
r_long_range_B_refined7.894
r_long_range_B_other7.891
r_dihedral_angle_1_deg6.9
r_scangle_other6.266
r_scbond_it4.182
r_scbond_other4.182
r_mcangle_it3.999
r_mcangle_other3.999
r_mcbond_it2.768
r_mcbond_other2.767
r_angle_refined_deg1.863
r_angle_other_deg1.108
r_chiral_restr0.101
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms7967
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing