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LecA from Pseudomonas aeruginosa in complex with a catechol CAS no. 61445-50-9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 292.15 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound for co-crystallisation
Crystal Properties Matthews coefficient Solvent content 1.92 36.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.222 α = 90 b = 76.066 β = 90 c = 107.148 γ = 90
Symmetry Space Group P 21 2 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 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.84 48.22 99.9 0.068 0.071 0.019 0.999 23.9 13.4 35137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.88 97.9 0.469 0.488 0.133 0.943 13.1
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 1OKO 1.84 44.01 33319 1776 99.82 0.1945 0.1929 0.2024 0.2255 0.2313 RANDOM 21.196
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] -0.43 0.71 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.501 r_dihedral_angle_4_deg 20.038 r_dihedral_angle_3_deg 10.736 r_dihedral_angle_1_deg 7.037 r_angle_refined_deg 1.545 r_angle_other_deg 1.459 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.501 r_dihedral_angle_4_deg 20.038 r_dihedral_angle_3_deg 10.736 r_dihedral_angle_1_deg 7.037 r_angle_refined_deg 1.545 r_angle_other_deg 1.459 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3578 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 58
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing