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FimH in complex with alpha1,6 core-fucosylated oligomannose-3, crystallized in the trigonal space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 1.1 M Lithium sulphate; 0.1 M Tris-HCl pH 9.0; 10 mM nickel chloride
Crystal Properties Matthews coefficient Solvent content 2.65 53.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.056 α = 90 b = 91.056 β = 90 c = 79.578 γ = 120
Symmetry Space Group P 31 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 EIGER X 16M 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.987 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.45 56.076 95.16 0.075 0.077 0.017 0.9996 19.325 20.11 56199 24.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.556 21.9 1.837 1.949 0.639 0.615 1.6 16.95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 56.076 56198 1481 82.867 0.155 0.1532 0.152 0.2054 0.2045 32.691
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] 0.603 0.301 0.603 -1.955
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 23.863 r_dihedral_angle_6_deg 17.432 r_scbond_it 16.344 r_scangle_it 13.632 r_dihedral_angle_3_deg 11.962 r_lrange_it 10.166 r_dihedral_angle_1_deg 8.084 r_dihedral_angle_2_deg 5.984 r_mcangle_it 5.584 r_mcbond_it 5.091
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 23.863 r_dihedral_angle_6_deg 17.432 r_scbond_it 16.344 r_scangle_it 13.632 r_dihedral_angle_3_deg 11.962 r_lrange_it 10.166 r_dihedral_angle_1_deg 8.084 r_dihedral_angle_2_deg 5.984 r_mcangle_it 5.584 r_mcbond_it 5.091 r_angle_refined_deg 1.809 r_chiral_restr 0.437 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.217 r_xyhbond_nbd_refined 0.214 r_nbd_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.159 r_ncsr_local_group_1 0.113 r_metal_ion_refined 0.035 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2392 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHENIX model building autoPROC data processing XDS data reduction XSCALE data scaling PHASER phasing