4IIV

Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.5 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 bromide, 0.1 M Bis-Tris propane, pH 8.5, 27.5% w/v PEG3350, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5351.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.477α = 90
b = 127.477β = 90
c = 122.951γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2012-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

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
12.5501000.08830.31339057-338.7
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)
12.52.541000.8233.312.71943

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 3OSU2.541.7637974189997.170.18240.18040.2198RANDOM35.2639
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]
-0.3-0.3-0.30.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.971
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg14.652
r_dihedral_angle_1_deg5.515
r_angle_refined_deg1.51
r_angle_other_deg1.129
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.971
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg14.652
r_dihedral_angle_1_deg5.515
r_angle_refined_deg1.51
r_angle_other_deg1.129
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7023
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms192

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling