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Structure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the supernatant after centrifugation at 20000 g for 5 minutes since precipitation was observed and a crystallization solution containing 18% PEG3350, 150 mM potassium thiocyanate (KSCN) and 100 mM Tris HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.26 α = 90 b = 61.932 β = 90 c = 180.008 γ = 90
Symmetry Space Group P 21 21 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 2020-02-06 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 1.75 45 100 0.067 0.08 0.043 0.998 16.1 6.3 48775
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 1.75 1.78 99.9 0.291 0.347 0.186 0.976 5.3 6.4
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 1OKO 1.75 43.131 48697 2506 99.938 0.164 0.1613 0.2074 0.2105 13.085
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] 1.167 0.827 -1.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.996 r_dihedral_angle_3_deg 12.109 r_dihedral_angle_1_deg 6.603 r_dihedral_angle_4_deg 5.676 r_lrange_it 4.889 r_lrange_other 4.306 r_scangle_it 3.166 r_scangle_other 3.165 r_scbond_other 2.158 r_scbond_it 2.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.996 r_dihedral_angle_3_deg 12.109 r_dihedral_angle_1_deg 6.603 r_dihedral_angle_4_deg 5.676 r_lrange_it 4.889 r_lrange_other 4.306 r_scangle_it 3.166 r_scangle_other 3.165 r_scbond_other 2.158 r_scbond_it 2.157 r_mcangle_other 2.118 r_mcangle_it 2.117 r_angle_refined_deg 1.809 r_angle_other_deg 1.57 r_mcbond_it 1.509 r_mcbond_other 1.505 r_nbd_refined 0.199 r_symmetry_nbd_other 0.191 r_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.166 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.117 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.065 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3602 Nucleic Acid Atoms Solvent Atoms 833 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing