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Structural basis of Lewisb antigen binding by the Helicobacter pylori adhesin BabA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 22% PEG 3350, 0.1 M PCTP (pH = 6.0)
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.59 α = 90 b = 91.77 β = 90 c = 96.42 γ = 90
Symmetry Space Group P 21 21 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 2M 2014-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92 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 2.12 44.78 98.9 0.141 11.8 6.6 29319
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 2.12 2.18 0.643 4.9
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 4ZHO 2.12 44.78 29319 1513 98.86 0.17357 0.17102 0.1805 0.22259 0.2343 RANDOM 27.888
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] -1.73 3.04 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.6 r_dihedral_angle_4_deg 14.246 r_dihedral_angle_3_deg 12.826 r_long_range_B_refined 6.549 r_long_range_B_other 6.515 r_dihedral_angle_1_deg 5.46 r_scangle_other 5.144 r_mcangle_it 3.388 r_mcangle_other 3.387 r_scbond_it 3.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.6 r_dihedral_angle_4_deg 14.246 r_dihedral_angle_3_deg 12.826 r_long_range_B_refined 6.549 r_long_range_B_other 6.515 r_dihedral_angle_1_deg 5.46 r_scangle_other 5.144 r_mcangle_it 3.388 r_mcangle_other 3.387 r_scbond_it 3.279 r_scbond_other 3.278 r_mcbond_it 2.246 r_mcbond_other 2.233 r_angle_refined_deg 1.747 r_angle_other_deg 1.004 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 3655 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction