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Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DCQ PDB ENTRY 3DCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 330 MM SODIUM CACODYLATE PH 6.5 200 MM AMMONIUM SULPHATE 30% PEG8K
Crystal Properties Matthews coefficient Solvent content 1.89 34.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.53 α = 90 b = 76.98 β = 90 c = 99.66 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 PILATUS 6M KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL 2012-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.41 42.25 99.8 0.07 19.2 7.2 76102 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.47 98.8 0.65 3.1 7
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 (Observed) 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 PDB ENTRY 3DCQ 1.41 42.24 72296 3805 99.78 0.11614 0.1146 0.1262 0.14529 0.1514 RANDOM 13.07
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] 0.14 0.95 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.613 r_dihedral_angle_4_deg 19.432 r_sphericity_free 17.879 r_dihedral_angle_3_deg 9.818 r_rigid_bond_restr 7.724 r_dihedral_angle_1_deg 6.692 r_sphericity_bonded 4.798 r_scbond_it 2.009 r_angle_refined_deg 1.651 r_angle_other_deg 1.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.613 r_dihedral_angle_4_deg 19.432 r_sphericity_free 17.879 r_dihedral_angle_3_deg 9.818 r_rigid_bond_restr 7.724 r_dihedral_angle_1_deg 6.692 r_sphericity_bonded 4.798 r_scbond_it 2.009 r_angle_refined_deg 1.651 r_angle_other_deg 1.475 r_mcangle_it 1.27 r_mcbond_it 1.135 r_mcbond_other 1.135 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.249 r_symmetry_vdw_other 0.216 r_nbd_other 0.204 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.104 r_nbtor_other 0.084 r_metal_ion_refined 0.063 r_symmetry_hbond_refined 0.033 r_bond_refined_d 0.015 r_bond_other_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing