4IIU

Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.1 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OSUPDB ENTRY 3OSU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52890.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6453.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.541α = 90
b = 128.541β = 90
c = 125.938γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2012-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

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
12.1501000.06245.311.268701-326.1
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)
12.12.141000.8193.510.63403

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 3OSU2.139.9467856342798.660.16920.16790.1925RANDOM34.3943
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]
-0.43-0.43-0.431.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.52
r_dihedral_angle_4_deg14.55
r_dihedral_angle_3_deg13.193
r_dihedral_angle_1_deg5.396
r_angle_refined_deg1.448
r_angle_other_deg1.03
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.52
r_dihedral_angle_4_deg14.55
r_dihedral_angle_3_deg13.193
r_dihedral_angle_1_deg5.396
r_angle_refined_deg1.448
r_angle_other_deg1.03
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7016
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms192

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing