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Co-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF7
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 4 293 1 M (NH4)2 SO4, 90 mM Na-citrate pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.12 41.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.31 α = 90 b = 78.61 β = 90 c = 108.935 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 CCD ADSC QUANTUM 315r 2013-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98 SOLEIL PROXIMA 2
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 1.88 44.77 97.4 11.2 5.7 21548
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) 1.88 1.98 85.6 0.951 2.1 5.3 2703
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 1.88 63.75 20400 1087 97.13 0.18759 0.18552 0.1979 0.22601 0.2368 RANDOM 31.457
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] 2.34 -0.09 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_4_deg 16.333 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_1_deg 8.364 r_long_range_B_refined 6.229 r_long_range_B_other 6.226 r_scangle_other 4.347 r_scbond_it 2.834 r_scbond_other 2.833 r_mcangle_it 2.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_4_deg 16.333 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_1_deg 8.364 r_long_range_B_refined 6.229 r_long_range_B_other 6.226 r_scangle_other 4.347 r_scbond_it 2.834 r_scbond_other 2.833 r_mcangle_it 2.758 r_mcangle_other 2.758 r_angle_refined_deg 1.994 r_mcbond_it 1.883 r_mcbond_other 1.88 r_angle_other_deg 0.94 r_chiral_restr 0.14 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.005 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 2028 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building