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Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group H Lewis b hexasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M sodium nitrate, 0.1M Bis Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.096 α = 90 b = 131.889 β = 94.77 c = 123.102 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96863 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.72 45 99.8 0.16 6.7 4 43591 38.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.89 99.8 2.6 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5F7K 2.72 45 41291 2194 99.46 0.18098 0.17898 0.1891 0.21767 0.2251 RANDOM 49.465
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] 0.95 0.53 0.95 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_4_deg 22.471 r_dihedral_angle_3_deg 17.925 r_dihedral_angle_1_deg 6.682 r_long_range_B_refined 5.94 r_long_range_B_other 5.912 r_scangle_other 4.248 r_mcangle_it 3.181 r_mcangle_other 3.181 r_scbond_it 2.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_4_deg 22.471 r_dihedral_angle_3_deg 17.925 r_dihedral_angle_1_deg 6.682 r_long_range_B_refined 5.94 r_long_range_B_other 5.912 r_scangle_other 4.248 r_mcangle_it 3.181 r_mcangle_other 3.181 r_scbond_it 2.613 r_scbond_other 2.612 r_mcbond_it 1.904 r_mcbond_other 1.904 r_angle_refined_deg 1.646 r_angle_other_deg 0.992 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 Atoms Number Protein Atoms 7974 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing