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Co-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B4P 4B4P and 2X1O experimental model PDB 2X1O 4B4P and 2X1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 2 M (NH4)2 SO4, 5% PEG-400 and 100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.562 α = 90 b = 102.961 β = 90 c = 114.528 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2011-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
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 1.57 46.95 98.6 11.1 9.7 42810
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) 1.57 1.66 95.5 1.837 1 9.5 5989
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4B4P and 2X1O 1.57 57.26 40616 2157 98.42 0.19648 0.19497 0.22567 0.2108 RANDOM 23.383
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] -0.42 -0.08 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_3_deg 13.899 r_dihedral_angle_4_deg 12.435 r_dihedral_angle_1_deg 7.056 r_long_range_B_refined 6.394 r_long_range_B_other 6.107 r_scangle_other 3.035 r_scbond_it 2.113 r_scbond_other 2.007 r_angle_refined_deg 1.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_3_deg 13.899 r_dihedral_angle_4_deg 12.435 r_dihedral_angle_1_deg 7.056 r_long_range_B_refined 6.394 r_long_range_B_other 6.107 r_scangle_other 3.035 r_scbond_it 2.113 r_scbond_other 2.007 r_angle_refined_deg 1.968 r_mcangle_it 1.798 r_mcangle_other 1.798 r_mcbond_it 1.192 r_mcbond_other 1.187 r_angle_other_deg 0.91 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 2089 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building