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Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group B Lewis b heptasaccharide
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 3.22 61.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.09 α = 90 b = 132.44 β = 94.93 c = 123.51 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 I04 0.96863 Diamond I04
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 2.81 43.2 99.7 0.08 12.5 4.6 39799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.88 99.9 0.751 1.8 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5F7K 2.81 43.2 37751 2026 99.57 0.17263 0.1707 0.20753 0.2044 RANDOM 74.223
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 -0.23 0.65 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.52 r_dihedral_angle_4_deg 21.182 r_dihedral_angle_3_deg 17.566 r_long_range_B_refined 7.934 r_long_range_B_other 7.934 r_dihedral_angle_1_deg 6.475 r_scangle_other 6.174 r_mcangle_it 4.858 r_mcangle_other 4.857 r_scbond_it 3.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.52 r_dihedral_angle_4_deg 21.182 r_dihedral_angle_3_deg 17.566 r_long_range_B_refined 7.934 r_long_range_B_other 7.934 r_dihedral_angle_1_deg 6.475 r_scangle_other 6.174 r_mcangle_it 4.858 r_mcangle_other 4.857 r_scbond_it 3.962 r_scbond_other 3.961 r_mcbond_it 3.146 r_mcbond_other 3.146 r_angle_refined_deg 1.622 r_angle_other_deg 0.94 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 7970 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing