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Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with alpha-methyl-fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A6Q PDB ENTRY 5A6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.8 26% PEG 8K 1M LICL 0.1M CITRIC ACID PH 3.8
Crystal Properties Matthews coefficient Solvent content 2.02 39.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.558 α = 90 b = 65.585 β = 90 c = 109.036 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 CCD ADSC QUANTUM 315r 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.55 37.84 99.9 0.07 20.9 6.4 55470 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 1.55 1.58 98.5 0.39 3.4 4.6
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 5A6Q 1.55 37.84 52637 2763 99.87 0.12944 0.12818 0.1406 0.1534 0.164 RANDOM 9.03
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] 0.47 -0.15 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.241 r_dihedral_angle_3_deg 9.598 r_dihedral_angle_1_deg 6.844 r_dihedral_angle_4_deg 4.461 r_angle_other_deg 2.004 r_angle_refined_deg 1.641 r_scbond_it 1.252 r_mcangle_it 1.1 r_mcbond_it 0.694 r_mcbond_other 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.241 r_dihedral_angle_3_deg 9.598 r_dihedral_angle_1_deg 6.844 r_dihedral_angle_4_deg 4.461 r_angle_other_deg 2.004 r_angle_refined_deg 1.641 r_scbond_it 1.252 r_mcangle_it 1.1 r_mcbond_it 0.694 r_mcbond_other 0.694 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_bond_other_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 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_mcangle_other 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 3280 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing