3U0F

The structure of Beta-ketoacyl synthase from Brucella melitensis bound to the fragment 7-hydroxycoumarin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289BrabA.00113.a at 22.94 mg/ml. 0.2M Sodium malonate, 0.1M Bis tris propane pH8.5, 20% PEG3350. BrabA.00113.a.A1 PW25441, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.56α = 90
b = 83.25β = 121.2
c = 73.81γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
11.2539.27597.80.06115.27109758-313.707
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)
11.251.28930.353.63

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 DIFFRACTIONDirect phasing from previous structureTHROUGHOUT3LRF1.2539.275109671549797.970.12260.1220.1341RANDOM10.2718
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]
0.02-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.838
r_dihedral_angle_4_deg16.157
r_sphericity_free14.457
r_dihedral_angle_3_deg11.343
r_rigid_bond_restr9.49
r_dihedral_angle_1_deg6.175
r_sphericity_bonded3.872
r_angle_other_deg1.713
r_angle_refined_deg1.326
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.838
r_dihedral_angle_4_deg16.157
r_sphericity_free14.457
r_dihedral_angle_3_deg11.343
r_rigid_bond_restr9.49
r_dihedral_angle_1_deg6.175
r_sphericity_bonded3.872
r_angle_other_deg1.713
r_angle_refined_deg1.326
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3016
Nucleic Acid Atoms
Solvent Atoms520
Heterogen Atoms19

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing