2EZT

Pyruvate oxidase variant F479W in complex with reaction intermediate 2-hydroxyethyl-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 = 118.79α = 90
b = 154.022β = 90
c = 165.32γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2005-05-05MSINGLE 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
12.299999.20.1818.934.6680806808023.719.5
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)
12.292.3299.699.60.4443.34.1

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 1POW2.2994.07226808068079137999.1440.1510.1510.14980.1873RANDOM11.447
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]
0.702-0.516-0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.249
r_dihedral_angle_4_deg18.9
r_dihedral_angle_3_deg14.021
r_dihedral_angle_1_deg6.339
r_scangle_it3.537
r_scbond_it2.144
r_angle_refined_deg1.508
r_mcangle_it1.131
r_mcbond_it0.578
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.249
r_dihedral_angle_4_deg18.9
r_dihedral_angle_3_deg14.021
r_dihedral_angle_1_deg6.339
r_scangle_it3.537
r_scbond_it2.144
r_angle_refined_deg1.508
r_mcangle_it1.131
r_mcbond_it0.578
r_nbtor_refined0.299
r_symmetry_vdw_refined0.216
r_nbd_refined0.199
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.13
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9046
Nucleic Acid Atoms
Solvent Atoms948
Heterogen Atoms190

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing