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Structure of the PAIL lectin from Pseudomonas aeruginosa in complex with 2-Naphtyl-1-thio-beta-D-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO PDB ENTRY 1OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.8 M LISO4, 100 MM SODIUM ACETATE PH 4.5, 25% GLYCEROL (ADDED FOR CRYPROTECTION).
Crystal Properties Matthews coefficient Solvent content 3.06 59.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.334 α = 90 b = 54.334 β = 90 c = 390.501 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.15 40 99.5 0.04 14.4 3.5 37963 2 40
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 2.15 2.27 99.9 0.39 2.3 3.5
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 1OKO 2.15 38.13 35959 1888 99.26 0.21657 0.21437 0.2122 0.25881 0.2559 RANDOM 44.949
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] 2.35 1.17 2.35 -3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_4_deg 11.275 r_dihedral_angle_1_deg 6.464 r_angle_refined_deg 1.657 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_4_deg 11.275 r_dihedral_angle_1_deg 6.464 r_angle_refined_deg 1.657 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.156 r_metal_ion_refined 0.127 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3604 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing