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Blood group antigen binding adhesin BabA of Helicobacter pylori strain P436 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 8 293 1 M Sodium acetate, 100 mM Imidazole pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.1 70.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.047 α = 90 b = 136.167 β = 90 c = 124.634 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M 2015-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 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 2.44 51.54 100 0.095 8.8 6.5 39582
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 2.44 2.57 100 1.7 6.4
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 2.44 51.54 37277 1996 99.26 0.2073 0.2048 0.2084 0.25744 0.2599 RANDOM 57.443
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] 0.27 0.9 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.294 r_dihedral_angle_4_deg 19.705 r_dihedral_angle_3_deg 16.28 r_long_range_B_refined 7.34 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 6.732 r_scangle_other 5.997 r_mcangle_it 4.301 r_mcangle_other 4.3 r_scbond_it 3.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.294 r_dihedral_angle_4_deg 19.705 r_dihedral_angle_3_deg 16.28 r_long_range_B_refined 7.34 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 6.732 r_scangle_other 5.997 r_mcangle_it 4.301 r_mcangle_other 4.3 r_scbond_it 3.975 r_scbond_other 3.975 r_mcbond_it 2.881 r_mcbond_other 2.879 r_angle_refined_deg 1.877 r_angle_other_deg 0.988 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3966 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing