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FimH lectin domain in complex with mannose C-linked to quinoline
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 5.5 293.15 3.0M NaCl and 0.1M BIS-TRIS at pH=5.5
Crystal Properties Matthews coefficient Solvent content 5.53 77.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.784 α = 90 b = 151.784 β = 90 c = 225.034 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 EIGER X 16M 2019-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.995 49.732 98.6 0.464 0.996 12.41 39.4 31057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 98.3 3.422 0.615 1.37 40.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.995 49.732 28931 1439 91.874 0.254 0.2512 0.2559 0.3034 0.309 RANDOM 53.611
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] -0.117 -0.059 -0.117 0.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.291 r_dihedral_angle_6_deg 16.377 r_dihedral_angle_2_deg 15.735 r_lrange_it 11.972 r_lrange_other 11.971 r_dihedral_angle_1_deg 8.665 r_mcangle_it 8.352 r_mcangle_other 8.35 r_scangle_it 7.264 r_scangle_other 7.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.291 r_dihedral_angle_6_deg 16.377 r_dihedral_angle_2_deg 15.735 r_lrange_it 11.972 r_lrange_other 11.971 r_dihedral_angle_1_deg 8.665 r_mcangle_it 8.352 r_mcangle_other 8.35 r_scangle_it 7.264 r_scangle_other 7.264 r_mcbond_it 5.497 r_mcbond_other 5.494 r_scbond_it 4.698 r_scbond_other 4.697 r_angle_refined_deg 1.387 r_angle_other_deg 0.506 r_nbd_other 0.251 r_xyhbond_nbd_refined 0.227 r_symmetry_nbd_other 0.206 r_symmetry_xyhbond_nbd_refined 0.2 r_nbd_refined 0.191 r_nbtor_refined 0.178 r_ncsr_local_group_5 0.15 r_ncsr_local_group_1 0.145 r_ncsr_local_group_4 0.14 r_ncsr_local_group_2 0.138 r_ncsr_local_group_6 0.122 r_ncsr_local_group_3 0.119 r_symmetry_nbd_refined 0.118 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.058 r_bond_other_d 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing