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STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2-Thiophenesulfonamide-N-(beta-L-fucopyranosyl methyl)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.8 292 20% PEG6K 0.5M LiCl 0.1M citric acid ph 3.8
Crystal Properties Matthews coefficient Solvent content 2.08 40.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.089 α = 90 b = 65.52 β = 90 c = 109.173 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 2014-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97712 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 38.59 98.2 0.053 0.998 20.5 5.7 45743 2 7.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 82.7 0.22 0.835 4.1 2.7
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 5a6q 1.65 38.59 43462 2221 98.03 0.13646 0.1346 0.1477 0.173 0.1786 RANDOM 11.838
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] 0.89 -0.14 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.067 r_dihedral_angle_4_deg 22.133 r_dihedral_angle_3_deg 10.649 r_dihedral_angle_1_deg 6.655 r_long_range_B_refined 4.936 r_long_range_B_other 4.398 r_scangle_other 2.6 r_angle_other_deg 1.871 r_scbond_it 1.73 r_scbond_other 1.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.067 r_dihedral_angle_4_deg 22.133 r_dihedral_angle_3_deg 10.649 r_dihedral_angle_1_deg 6.655 r_long_range_B_refined 4.936 r_long_range_B_other 4.398 r_scangle_other 2.6 r_angle_other_deg 1.871 r_scbond_it 1.73 r_scbond_other 1.729 r_angle_refined_deg 1.671 r_mcangle_it 1.362 r_mcangle_other 1.362 r_mcbond_it 0.905 r_mcbond_other 0.904 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_bond_other_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.008 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3282 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing