4JV3

Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LRFpdb entry 3LRF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290MD PACT screen, H2: 20% PEG 3350, 100mM BisTrisPropane pH 8.5, 200mM Na-bromide; tray 233841 f11, BrabA.00113.a at 23 mg/ml, 2.5mM platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.346.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.16α = 90
b = 84.48β = 120.81
c = 74.02γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+Rigaku VariMax2013-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.75098.50.03347.7911.24554544869-320.929
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)
11.71.7496.80.1877.52

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 3LRF1.742.284554544869226498.790.143820.14380.14250.1689RANDOM16.929
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]
-0.060.35-0.1-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.503
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg12.637
r_dihedral_angle_1_deg6.471
r_angle_refined_deg1.354
r_mcangle_it1.19
r_angle_other_deg0.766
r_mcbond_it0.736
r_mcbond_other0.734
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.503
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg12.637
r_dihedral_angle_1_deg6.471
r_angle_refined_deg1.354
r_mcangle_it1.19
r_angle_other_deg0.766
r_mcbond_it0.736
r_mcbond_other0.734
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3005
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms31

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XDSdata reduction