4BO2

Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 1-(1-ethylbenzimidazol-2- yl)-3-(2-methoxyphenyl)urea at 1.9A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BNWPDB ENTRY 4BNW, LIGAND-FREE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.8 M SUCCINIC ACID PH 7.0, 1 MM 1-(1-ETHYLBENZIMIDAZOL-2-YL)-3-(2-METHOXYPHENYL)UREA, FINAL PROTEIN CONCENTRATION 5 MG/ML
Crystal Properties
Matthews coefficientSolvent content
2.1242.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.55α = 90
b = 108.92β = 90
c = 149.72γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2012-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.938.5388.50.0712.34.167510-321.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.94560.324.33.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4BNW, LIGAND-FREE1.938.5663200336387.290.236710.234980.26923RANDOM39.625
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]
5.22-2.25-2.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.376
r_dihedral_angle_4_deg17.403
r_dihedral_angle_3_deg14.49
r_dihedral_angle_1_deg5.773
r_angle_refined_deg1.693
r_angle_other_deg1.475
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.376
r_dihedral_angle_4_deg17.403
r_dihedral_angle_3_deg14.49
r_dihedral_angle_1_deg5.773
r_angle_refined_deg1.693
r_angle_other_deg1.475
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.007
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 AtomsNumber
Protein Atoms6942
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing