2EZ8

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop5.7280ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.956.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.133α = 90
b = 154.462β = 90
c = 165.656γ = 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
11.9724.9698.20.10711.494.510561410559023.712.8
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)
11.9720.87187.10.2753.53.7

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 1POW1.96324.962105614105590210597.9640.1490.1490.14860.1722RANDOM13.078
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]
1.953-1.008-0.945
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.135
r_dihedral_angle_4_deg19.193
r_dihedral_angle_3_deg13.47
r_dihedral_angle_1_deg6.155
r_scangle_it3.715
r_scbond_it2.22
r_angle_refined_deg1.463
r_mcangle_it1.153
r_mcbond_it0.611
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.135
r_dihedral_angle_4_deg19.193
r_dihedral_angle_3_deg13.47
r_dihedral_angle_1_deg6.155
r_scangle_it3.715
r_scbond_it2.22
r_angle_refined_deg1.463
r_mcangle_it1.153
r_mcbond_it0.611
r_nbtor_refined0.301
r_nbd_refined0.199
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.117
r_chiral_restr0.093
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 Atoms993
Heterogen Atoms186

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing