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STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)
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 4.4 293.15 24% PEG 8K, 1M LiCl and 100 mM sodium acetate pH = 4.4
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.376 α = 101.809 b = 51.589 β = 99.474 c = 52.604 γ = 115.811
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 9M Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors 2022-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 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 1.5 40.69 95.5 0.051 0.072 0.051 0.997 12.9 3.4 211861
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 1.5 1.53 92.49 1.53 0.45 0.318 0.881 3.4 3.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5A3O 1.5 40.69 61588 7571 95.507 0.142 0.1383 0.1688 0.1828 random selection 15.5
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] 0.341 0.222 -0.038 0.097 0.067 -0.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.361 r_dihedral_angle_4_deg 17.432 r_dihedral_angle_3_deg 10.679 r_dihedral_angle_1_deg 7.066 r_lrange_other 4.748 r_lrange_it 4.747 r_scangle_it 3.413 r_scangle_other 3.412 r_scbond_it 2.334 r_scbond_other 2.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.361 r_dihedral_angle_4_deg 17.432 r_dihedral_angle_3_deg 10.679 r_dihedral_angle_1_deg 7.066 r_lrange_other 4.748 r_lrange_it 4.747 r_scangle_it 3.413 r_scangle_other 3.412 r_scbond_it 2.334 r_scbond_other 2.334 r_mcangle_it 1.907 r_mcangle_other 1.907 r_angle_refined_deg 1.824 r_angle_other_deg 1.609 r_mcbond_it 1.319 r_mcbond_other 1.314 r_nbd_refined 0.252 r_symmetry_nbd_refined 0.219 r_nbd_other 0.213 r_symmetry_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.103 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.068 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 3286 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing