3FK5

Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III, FabH (Xoo4209) from Xanthomonas oryzae pv. oryzae KACC10331


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HNJPDB ENTRY 1HNJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22870.1M HEPES pH 7.2, 30% PEG 6000, 5% 2-methyl-2, 4-pentanediol, 3% D-galactose , VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.3647.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.75α = 90
b = 79.45β = 90
c = 62.29γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1.00000PAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0529100217862063211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.052.1281.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HNJ2.0529217862063211111000.177220.177220.174170.23692RANDOM33.948
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]
0.01-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.859
r_dihedral_angle_4_deg17.969
r_dihedral_angle_3_deg15.533
r_dihedral_angle_1_deg6.233
r_scangle_it5.31
r_scbond_it3.378
r_mcangle_it1.998
r_angle_refined_deg1.9
r_mcbond_it1.151
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.859
r_dihedral_angle_4_deg17.969
r_dihedral_angle_3_deg15.533
r_dihedral_angle_1_deg6.233
r_scangle_it5.31
r_scbond_it3.378
r_mcangle_it1.998
r_angle_refined_deg1.9
r_mcbond_it1.151
r_chiral_restr0.143
r_bond_refined_d0.022
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2556
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling