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Blood group antigen binding adhesin BabA of Helicobacter pylori strain S831 in complex with Nanobody Nb-ER19
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 7.5 293 0.2 M potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.21 61.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.034 α = 90 b = 132.138 β = 94.9 c = 123.485 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 2014-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
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 2.59 48.5 97.7 0.051 9.4 3.6 49587
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 2.59 2.73 89.1 0.791 1.3 3
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 2.59 48.5 47074 2487 97.55 0.19655 0.19472 0.1982 0.23026 0.2313 RANDOM 68.566
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] -0.84 -0.77 1.06 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.143 r_dihedral_angle_4_deg 22.649 r_dihedral_angle_3_deg 17.574 r_long_range_B_refined 7.316 r_long_range_B_other 7.315 r_dihedral_angle_1_deg 6.41 r_scangle_other 5.678 r_mcangle_it 4.722 r_mcangle_other 4.722 r_scbond_it 3.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.143 r_dihedral_angle_4_deg 22.649 r_dihedral_angle_3_deg 17.574 r_long_range_B_refined 7.316 r_long_range_B_other 7.315 r_dihedral_angle_1_deg 6.41 r_scangle_other 5.678 r_mcangle_it 4.722 r_mcangle_other 4.722 r_scbond_it 3.691 r_scbond_other 3.691 r_mcbond_it 3.147 r_mcbond_other 3.147 r_angle_refined_deg 1.595 r_angle_other_deg 1.017 r_chiral_restr 0.082 r_bond_refined_d 0.014 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 7972 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing