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Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA)from Pseudomonas aeruginosa in complex with DDD00082063
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 PEG, Tris
Crystal Properties Matthews coefficient Solvent content 3.03 59.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.885 α = 90 b = 144.299 β = 116.26 c = 76.517 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 2M 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
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 1.96 83.85 94.3 0.058 0.999 12.5 3.7 59206
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 1.96 2.11 0.856 0.545
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4CL6 1.96 83.85 56392 2885 69.38 0.2108 0.2098 0.2312 0.2295 RANDOM 41.314
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] 0.23 -0.02 0.09 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.809 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_4_deg 15.134 r_dihedral_angle_1_deg 7.798 r_angle_refined_deg 1.546 r_angle_other_deg 1.297 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.809 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_4_deg 15.134 r_dihedral_angle_1_deg 7.798 r_angle_refined_deg 1.546 r_angle_other_deg 1.297 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6384 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing