2E77

Crystal structure of L-lactate oxidase with pyruvate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DU2PDB ENTRY 2DU2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPVAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2445.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.841α = 90
b = 118.566β = 121.07
c = 107.237γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.95099.50.053113367

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DU21.937.4107689567699.170.179030.176460.22682RANDOM25.131
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.505
r_dihedral_angle_3_deg15.953
r_dihedral_angle_4_deg14.366
r_dihedral_angle_1_deg6.433
r_scangle_it3.634
r_scbond_it2.384
r_angle_refined_deg1.661
r_mcangle_it1.379
r_mcbond_it0.902
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.505
r_dihedral_angle_3_deg15.953
r_dihedral_angle_4_deg14.366
r_dihedral_angle_1_deg6.433
r_scangle_it3.634
r_scbond_it2.384
r_angle_refined_deg1.661
r_mcangle_it1.379
r_mcbond_it0.902
r_nbtor_refined0.307
r_nbd_refined0.221
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.184
r_xyhbond_nbd_refined0.18
r_chiral_restr0.128
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11118
Nucleic Acid Atoms
Solvent Atoms1311
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing