2EZU

Pyruvate oxidase variant F479W in complex with reaction intermediate 2-acetyl-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 = 118.276α = 90
b = 154.724β = 90
c = 166.003γ = 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
12.162595.10.1169.464774117740223.715.8
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)
12.162.190.93293.20.2583.22.7

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 1POW2.162527741177402154395.1460.1440.1440.14310.1839RANDOM12.081
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]
1.389-0.523-0.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.187
r_dihedral_angle_4_deg17.813
r_dihedral_angle_3_deg13.496
r_dihedral_angle_1_deg6.32
r_scangle_it3.778
r_scbond_it2.344
r_angle_refined_deg1.521
r_mcangle_it1.197
r_mcbond_it0.64
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.187
r_dihedral_angle_4_deg17.813
r_dihedral_angle_3_deg13.496
r_dihedral_angle_1_deg6.32
r_scangle_it3.778
r_scbond_it2.344
r_angle_refined_deg1.521
r_mcangle_it1.197
r_mcbond_it0.64
r_nbtor_refined0.299
r_nbd_refined0.198
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.134
r_chiral_restr0.095
r_metal_ion_refined0.025
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9046
Nucleic Acid Atoms
Solvent Atoms977
Heterogen Atoms180

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing