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Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 1-(2-chlorophenyl)-3-(1- methylbenzimidazol-2-yl)urea at 2.5A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BNT PDB ENTRY 4BNT CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM MALONATE, 20% (W/V) PEG3350, 1 MM 1-(2-CHLOROPHENYL)-3-(1-METHYLBENZIMIDAZOL-2-YL)UREA, FINAL PROTEIN CONCENTRATION 3.3 MG/ML
Crystal Properties Matthews coefficient Solvent content 1.9 35.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.86 α = 90 b = 108.07 β = 90 c = 146.61 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2012-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.5 36.92 98.9 0.09 9.4 4.3 30064 -3 35.8
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 2.5 2.61 99.3 0.56 2.6 4.4
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 PDB ENTRY 4BNT CHAIN A 2.5 36.94 28514 1502 98.52 0.20685 0.20421 0.25697 0.2432 RANDOM 60.776
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] 0.65 -1.11 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.953 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_4_deg 14.052 r_mcangle_it 6.348 r_dihedral_angle_1_deg 5.414 r_scbond_it 5.109 r_mcbond_it 4.2 r_mcbond_other 4.199 r_angle_refined_deg 1.379 r_angle_other_deg 1.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.953 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_4_deg 14.052 r_mcangle_it 6.348 r_dihedral_angle_1_deg 5.414 r_scbond_it 5.109 r_mcbond_it 4.2 r_mcbond_other 4.199 r_angle_refined_deg 1.379 r_angle_other_deg 1.222 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 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 6862 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing