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FimH lectin domain in complex with oligomannose-6
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 8.5 291 1 M Lithium sulphate
100 mM Tris-HCl, pH 8.5
10 mM Nickel chloride
3% glycerol
Crystal Properties Matthews coefficient Solvent content 5.54 77.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.11 α = 90 b = 153.11 β = 90 c = 230.41 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER2 XE 16M MD3 diffractometer 2021-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97630 PETRA III, EMBL c/o DESY P14 (MX2)
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 3.186 114.925 88.45 0.613 0.643 0.188 0.9522 4.977 11.07 24701 1.2 69.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.186 3.341 34.1 1.767 1.838 0.584 0.502 1.6 13.067
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 3.186 114.925 24701 1532 87.916 0.207 0.2045 0.2088 0.2381 0.2424 61.211
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] -0.521 -0.261 -0.521 1.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.155 r_dihedral_angle_3_deg 14.77 r_lrange_it 9.711 r_lrange_other 9.711 r_scangle_it 8.107 r_scangle_other 8.106 r_dihedral_angle_1_deg 7.543 r_mcangle_it 7.365 r_mcangle_other 7.365 r_scbond_it 6.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.155 r_dihedral_angle_3_deg 14.77 r_lrange_it 9.711 r_lrange_other 9.711 r_scangle_it 8.107 r_scangle_other 8.106 r_dihedral_angle_1_deg 7.543 r_mcangle_it 7.365 r_mcangle_other 7.365 r_scbond_it 6.475 r_scbond_other 6.473 r_mcbond_it 5.302 r_mcbond_other 5.299 r_dihedral_angle_2_deg 5.211 r_angle_refined_deg 1.561 r_angle_other_deg 1.5 r_symmetry_nbd_other 1.042 r_nbd_other 0.314 r_symmetry_xyhbond_nbd_refined 0.303 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.164 r_ncsr_local_group_5 0.13 r_ncsr_local_group_1 0.129 r_ncsr_local_group_4 0.128 r_ncsr_local_group_2 0.118 r_ncsr_local_group_3 0.114 r_ncsr_local_group_6 0.096 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.058 r_bond_other_d 0.032 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_other 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing