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STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide (4i)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 28% PEG 8K, 200 mM (NH4)2SO4, 100 mM tris
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.909 α = 90 b = 76.495 β = 90 c = 184.306 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 PIXEL DECTRIS EIGER X 16M 2021-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 1.55 46.08 99.97 0.082 0.092 0.041 0.998 13.57 2 711298 18.9
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 1.55 1.58 0.557 0.092 0.272 0.902 3.43
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5A3O 1.55 46.076 73913 3662 99.984 0.144 0.1425 0.1659 0.1796 19.305
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] 0.928 -0.373 -0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.973 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 10.677 r_dihedral_angle_1_deg 7.293 r_lrange_it 4.575 r_lrange_other 4.247 r_scangle_it 3.375 r_scangle_other 3.367 r_scbond_it 2.405 r_scbond_other 2.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.973 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 10.677 r_dihedral_angle_1_deg 7.293 r_lrange_it 4.575 r_lrange_other 4.247 r_scangle_it 3.375 r_scangle_other 3.367 r_scbond_it 2.405 r_scbond_other 2.385 r_mcangle_it 1.789 r_mcangle_other 1.789 r_angle_refined_deg 1.717 r_angle_other_deg 1.577 r_mcbond_other 1.369 r_mcbond_it 1.368 r_nbd_refined 0.227 r_symmetry_nbd_other 0.202 r_nbd_other 0.173 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.125 r_ncsr_local_group_1 0.099 r_chiral_restr 0.098 r_symmetry_nbd_refined 0.098 r_ncsr_local_group_4 0.092 r_ncsr_local_group_2 0.091 r_ncsr_local_group_5 0.091 r_ncsr_local_group_6 0.091 r_symmetry_nbtor_other 0.088 r_ncsr_local_group_3 0.084 r_symmetry_xyhbond_nbd_refined 0.083 r_metal_ion_refined 0.065 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3294 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing