1Y9D

Pyruvate Oxidase variant V265A from Lactobacillus plantarum


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.856.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.66α = 90
b = 155.78β = 92.92
c = 100.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2003-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

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
12.227.30.06220.6147394

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1POW2.227.3147399139647736999.690.180680.177630.23794RANDOM46.443
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]
0.37-0.112.38-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.755
r_dihedral_angle_4_deg19.623
r_dihedral_angle_3_deg17.462
r_dihedral_angle_1_deg7.015
r_scangle_it4.428
r_scbond_it2.715
r_mcangle_it1.788
r_angle_refined_deg1.677
r_mcbond_it0.971
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.755
r_dihedral_angle_4_deg19.623
r_dihedral_angle_3_deg17.462
r_dihedral_angle_1_deg7.015
r_scangle_it4.428
r_scbond_it2.715
r_mcangle_it1.788
r_angle_refined_deg1.677
r_mcbond_it0.971
r_nbtor_refined0.308
r_symmetry_vdw_refined0.254
r_symmetry_hbond_refined0.247
r_nbd_refined0.232
r_xyhbond_nbd_refined0.204
r_chiral_restr0.12
r_metal_ion_refined0.062
r_bond_refined_d0.018
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_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 Atoms17318
Nucleic Acid Atoms
Solvent Atoms1848
Heterogen Atoms238

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing