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Crystal structure of FimH lectin domain bound to biphenyl mannoside meta-methyl ester.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UWF PDB entry 1UWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Co-crystallized FimH/mannoside 8a in 20% ethanol, 100mM imidazole pH 8.0, 200mM MgCl2.
Crystals diffract only after incubation in stabilizing solution containing
15% ethanol, 100mM imidazole pH 8.0, 200mM MgCl2, 10% PEG200, 5% glycerol and 1mM
compound 8a, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.2 70.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.82 α = 90 b = 198.82 β = 90 c = 198.82 γ = 90
Symmetry Space Group P 41 3 2
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 NOIR-1 2009-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
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 2.9 70.3 100 0.038 15.8 35.3 30391 30391 2 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1UWF 2.9 59.95 30391 28548 1526 99.1 0.22039 0.21904 0.2213 0.24516 0.2421 RANDOM 48.316
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.993 r_dihedral_angle_4_deg 23.585 r_dihedral_angle_3_deg 19.268 r_dihedral_angle_1_deg 11.243 r_angle_refined_deg 1.303 r_angle_other_deg 0.703 r_chiral_restr 0.067 r_mcbond_it 0.027 r_mcbond_other 0.021 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.993 r_dihedral_angle_4_deg 23.585 r_dihedral_angle_3_deg 19.268 r_dihedral_angle_1_deg 11.243 r_angle_refined_deg 1.303 r_angle_other_deg 0.703 r_chiral_restr 0.067 r_mcbond_it 0.027 r_mcbond_other 0.021 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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_mcangle_it r_scbond_it 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 4758 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 137
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling