4KGD

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FEEPDB ENTRY 4FEE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62801.5 M ammonium sulfate, 200 mM phosphate, 0.1 mM thiamine diphosphate, 1 mM magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.8757.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.28α = 90
b = 154.16β = 90
c = 165.47γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rToroidal focusing mirror2011-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.979200ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.063594.90.070.0819.683.38645341645341-310.593
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)
11.061.1393.20.522.21

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE RPDB ENTRY 4FEE1.06306259666453411936191.60.12710.12710.1505RANDOM12.8418
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
2858946.4211037.47
RMS Deviations
KeyRefinement Restraint Deviation
s_angle_d310
s_zero_chiral_vol79
s_non_zero_chiral_vol6
s_approx_iso_adps0.105
s_anti_bump_dis_restr0.087
s_similar_adp_cmpnt0.046
s_from_restr_planes0.037
s_bond_d0.015
s_similar_dist
s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9048
Nucleic Acid Atoms
Solvent Atoms1899
Heterogen Atoms225

Software

Software
Software NamePurpose
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
PHENIXphasing
SHELXLrefinement