2EZ9

Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1POWpdb entry 1POW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.7280ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.956.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.661α = 90
b = 154.517β = 90
c = 165.64γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2005-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.619.62830.08912.144.616538816534023.712.9
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)
11.61.620.75975.90.3432.43.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1POW1.619.622165388165339332882.9420.1590.1590.15830.1804RANDOM13.157
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]
1.141-0.663-0.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.842
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg12.261
r_dihedral_angle_1_deg5.867
r_scangle_it2.891
r_scbond_it1.736
r_angle_refined_deg1.318
r_mcangle_it0.918
r_mcbond_it0.47
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.842
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg12.261
r_dihedral_angle_1_deg5.867
r_scangle_it2.891
r_scbond_it1.736
r_angle_refined_deg1.318
r_mcangle_it0.918
r_mcbond_it0.47
r_nbtor_refined0.303
r_nbd_refined0.198
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.102
r_xyhbond_nbd_refined0.095
r_chiral_restr0.082
r_metal_ion_refined0.025
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9046
Nucleic Acid Atoms
Solvent Atoms1030
Heterogen Atoms178

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing