3STX

Crystal Structure of tomato Methylketone Synthase I H243A variant complexed with beta-ketoheptanoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7YAS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72770.1M MOPSO-Na+, 15% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, overnight soak in 1mM beta-ketoheptanoate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.237α = 90
b = 94.387β = 97.59
c = 60.077γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2

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
12.319.688.80.11811.194.12109721096-332.115

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 REPLACEMENTTHROUGHOUT7YAS2.319.37210972109310830.2350.20860.20520.2728RANDOM28.3783
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.208
r_dihedral_angle_3_deg15.441
r_dihedral_angle_4_deg13.444
r_dihedral_angle_1_deg5.361
r_scangle_it1.445
r_angle_refined_deg1.111
r_scbond_it0.885
r_mcangle_it0.865
r_mcbond_it0.476
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.208
r_dihedral_angle_3_deg15.441
r_dihedral_angle_4_deg13.444
r_dihedral_angle_1_deg5.361
r_scangle_it1.445
r_angle_refined_deg1.111
r_scbond_it0.885
r_mcangle_it0.865
r_mcbond_it0.476
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3944
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms20

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
XDSdata reduction
XDSdata scaling
CNSphasing