2YR6

Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YR4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1M HEPES pH7.5, 1.0M ammonium sulfate, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.877α = 90
b = 113.029β = 90
c = 136.463γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon 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
11.3534.1899.90.0895.5339311
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)
11.351.421000.3425.3

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 REPLACEMENTTHROUGHOUT2YR41.3534.183220711713299.820.104390.102630.13769RANDOM12.85
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]
0.75-0.35-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.62
r_sphericity_free24.119
r_dihedral_angle_4_deg21.295
r_dihedral_angle_3_deg11.858
r_sphericity_bonded8.167
r_scangle_it7.15
r_dihedral_angle_1_deg6.744
r_scbond_it5.765
r_mcangle_it3.911
r_mcbond_it3.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.62
r_sphericity_free24.119
r_dihedral_angle_4_deg21.295
r_dihedral_angle_3_deg11.858
r_sphericity_bonded8.167
r_scangle_it7.15
r_dihedral_angle_1_deg6.744
r_scbond_it5.765
r_mcangle_it3.911
r_mcbond_it3.339
r_rigid_bond_restr2.928
r_angle_refined_deg2.475
r_angle_other_deg1.27
r_mcbond_other1.153
r_symmetry_hbond_refined0.318
r_nbd_refined0.251
r_symmetry_vdw_other0.251
r_xyhbond_nbd_refined0.238
r_nbd_other0.225
r_symmetry_vdw_refined0.202
r_nbtor_refined0.193
r_chiral_restr0.174
r_nbtor_other0.097
r_xyhbond_nbd_other0.046
r_bond_refined_d0.031
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10424
Nucleic Acid Atoms
Solvent Atoms1957
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling