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Co-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 160 mM NaCl, 80 mM Bis-Tris pH 5.5, 20% PEG-3350
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.361 α = 90 b = 101.361 β = 90 c = 62.768 γ = 120
Symmetry Space Group P 32 2 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 2012-05-05 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) 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 2.51 87.8 99.9 12.6 10.9 13039
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 2.51 2.64 99.4 1.029 2.7 10.8 1868
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 2X1O 2.51 87.78 12390 633 99.78 0.19974 0.19705 0.2029 0.2542 0.2598 RANDOM 32.773
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] -0.26 -0.13 -0.26 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.227 r_dihedral_angle_3_deg 16.684 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_1_deg 7.787 r_long_range_B_refined 3.955 r_long_range_B_other 3.934 r_scangle_other 1.91 r_angle_refined_deg 1.869 r_mcangle_it 1.689 r_mcangle_other 1.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.227 r_dihedral_angle_3_deg 16.684 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_1_deg 7.787 r_long_range_B_refined 3.955 r_long_range_B_other 3.934 r_scangle_other 1.91 r_angle_refined_deg 1.869 r_mcangle_it 1.689 r_mcangle_other 1.688 r_scbond_it 1.162 r_scbond_other 1.161 r_mcbond_it 0.983 r_mcbond_other 0.983 r_angle_other_deg 0.849 r_chiral_restr 0.099 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 2001 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building PHASER phasing