4XOX

Structure of beta-ketoacyl-ACP synthase I (FabB) from Vibrio Cholerae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OYT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72891.6 M Ammonium citrate
Crystal Properties
Matthews coefficientSolvent content
2.3848.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.756α = 90
b = 88.654β = 90
c = 167.258γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2013-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97927APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
122794.30.050.0550.02416.34.951875
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03790.1340.1550.0770.973.12125

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 REPLACEMENTTHROUGHOUT3OYT2.012749221249293.670.15030.1490.1767RANDOM26.701
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]
-0.220.85-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.218
r_dihedral_angle_4_deg16.525
r_dihedral_angle_3_deg13.193
r_dihedral_angle_1_deg6.14
r_angle_refined_deg1.591
r_mcangle_it1.416
r_angle_other_deg1.308
r_mcbond_it0.867
r_mcbond_other0.867
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.218
r_dihedral_angle_4_deg16.525
r_dihedral_angle_3_deg13.193
r_dihedral_angle_1_deg6.14
r_angle_refined_deg1.591
r_mcangle_it1.416
r_angle_other_deg1.308
r_mcbond_it0.867
r_mcbond_other0.867
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5936
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms

Software

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