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Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with Nanobody Nb-ER19
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 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.99 α = 90 b = 131.66 β = 94.77 c = 123.46 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 PILATUS 6M-F 2014-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 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 2.17 58.04 99.4 0.046 15.6 4.5 85215 40.4
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 2.17 2.23 100 0.61 2.2 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.17 58.04 80920 4261 99.4 0.17259 0.17074 0.1778 0.20654 0.2107 RANDOM 54.385
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] -0.2 -0.14 0.2 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.002 r_dihedral_angle_4_deg 21.073 r_dihedral_angle_3_deg 15.745 r_long_range_B_refined 8.042 r_long_range_B_other 8.034 r_dihedral_angle_1_deg 6.369 r_scangle_other 5.797 r_scbond_it 4.065 r_scbond_other 3.981 r_mcangle_it 3.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.002 r_dihedral_angle_4_deg 21.073 r_dihedral_angle_3_deg 15.745 r_long_range_B_refined 8.042 r_long_range_B_other 8.034 r_dihedral_angle_1_deg 6.369 r_scangle_other 5.797 r_scbond_it 4.065 r_scbond_other 3.981 r_mcangle_it 3.894 r_mcangle_other 3.893 r_mcbond_it 2.842 r_mcbond_other 2.842 r_angle_refined_deg 1.859 r_angle_other_deg 1.186 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 8000 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing