4I08

Crystal structure of beta-ketoacyl-acyl carrier protein reductase (FabG) from Vibrio cholerae in complex with NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RROPDB ENTRY 3RRO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION92892.7M Ammonium Sulfate, 0.1M Tris-HCl, 2% PEG400, pH 9, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1342.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.941α = 90
b = 63.941β = 90
c = 190.374γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2011-03-18MSINGLE 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
12.065099.90.1029.55.627006-320.5
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)
12.062.11000.8114.91324

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 3RRO2.06347.8626944133099.790.15350.15260.171RANDOM38.6873
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]
11.8711.87-23.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.331
r_dihedral_angle_3_deg14.036
r_dihedral_angle_4_deg12.749
r_dihedral_angle_1_deg5.804
r_angle_refined_deg1.343
r_angle_other_deg0.825
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.331
r_dihedral_angle_3_deg14.036
r_dihedral_angle_4_deg12.749
r_dihedral_angle_1_deg5.804
r_angle_refined_deg1.343
r_angle_other_deg0.825
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3546
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms154

Software

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