4L9Z

Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, oxalate, and CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L9YPDB ENTRY 4L9Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52951 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M HEPES/NaOH, pH 7.5, 0.1 M magnesium chloride, 10% w/v PEG4000) + 1 part substrate solution (20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride, 20 mM propionyl-CoA, 25 mM sodium oxalate), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.3162.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 221.509α = 90
b = 221.509β = 90
c = 96.262γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.977408ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.01138.45598.30.15811.76.4175339175339
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.0112.12990.7440.74416.325641

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4L9Y2.01138.4550.86175323174491.880.17020.16990.19416.0823
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.899
f_angle_d0.881
f_chiral_restr0.059
f_bond_d0.006
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14274
Nucleic Acid Atoms
Solvent Atoms2526
Heterogen Atoms330

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHASERphasing