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Native structure of the LecB lectin from Pseudomonas aeruginosa strain PA14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UZV PDB ENTRY 1UZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 22% PEG 8K 0.2M AMSO4 0.1M TRIS PH 8.5 10 % GLYCEROL WAS ADDED AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.12 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.948 α = 90 b = 49.591 β = 93.37 c = 75.473 γ = 90
Symmetry Space Group P 1 21 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 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 1.7 41.42 99.7 0.08 10.1 3.2 43091 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 1.7 1.73 99.9 0.3 3.4 3.2
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 1UZV 1.7 41.42 40973 2104 99.6 0.15861 0.15669 0.1696 0.19698 0.2066 RANDOM 7.378
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] -0.11 0.08 0.08 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.657 r_dihedral_angle_3_deg 10.26 r_dihedral_angle_1_deg 6.491 r_angle_other_deg 1.957 r_angle_refined_deg 1.605 r_mcangle_it 1.115 r_scbond_it 0.979 r_mcbond_it 0.66 r_mcbond_other 0.66 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.657 r_dihedral_angle_3_deg 10.26 r_dihedral_angle_1_deg 6.491 r_angle_other_deg 1.957 r_angle_refined_deg 1.605 r_mcangle_it 1.115 r_scbond_it 0.979 r_mcbond_it 0.66 r_mcbond_other 0.66 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_bond_other_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_dihedral_angle_4_deg 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 3269 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing