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Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(cinnamido)-6-deoxy-alpha-D-mannopyranoside at 1.6 ansgtrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZDV PDB ENTRY 3ZDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.8 25% PEG 6K, 100MM CITRIC ACID PH 3.8 AND 1L LITHIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.954 α = 101.8 b = 51.111 β = 99.4 c = 52.348 γ = 115.95
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 CCD 2013-04-20 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 1.6 1.85 96.6 0.04 25.4 3.9 50076 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 1.6 1.63 90 0.18 6.1 3.7
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 3ZDV 1.6 39.25 47532 2541 96.6 0.16898 0.1671 0.178 0.20435 0.2132 RANDOM 8.769
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] 0.07 -0.29 0.04 0.04 0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.017 r_dihedral_angle_4_deg 16.805 r_dihedral_angle_3_deg 10.151 r_dihedral_angle_1_deg 7.111 r_angle_refined_deg 1.63 r_angle_other_deg 1.189 r_scbond_it 0.943 r_mcangle_it 0.935 r_mcbond_it 0.583 r_mcbond_other 0.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.017 r_dihedral_angle_4_deg 16.805 r_dihedral_angle_3_deg 10.151 r_dihedral_angle_1_deg 7.111 r_angle_refined_deg 1.63 r_angle_other_deg 1.189 r_scbond_it 0.943 r_mcangle_it 0.935 r_mcbond_it 0.583 r_mcbond_other 0.583 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 3303 Nucleic Acid Atoms Solvent Atoms 621 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing