5ZBD | pdb_00005zbd

Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1M MES, 40% Polyethylene glycol 400, pH6.8
Crystal Properties
Matthews coefficientSolvent content
2.3647.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.86α = 90
b = 89.27β = 90
c = 112.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.869.981000.0950.10314.457.3258268126.033
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91000.2740.2956.827.341

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.869.9878540414199.970.159810.157550.170.202250.21RANDOM22.401
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]
0.370.16-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.223
r_dihedral_angle_4_deg17.923
r_dihedral_angle_3_deg13.609
r_long_range_B_refined6.604
r_long_range_B_other6.429
r_dihedral_angle_1_deg6.109
r_scangle_other4.741
r_scbond_it3.079
r_scbond_other3.078
r_mcangle_it2.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.223
r_dihedral_angle_4_deg17.923
r_dihedral_angle_3_deg13.609
r_long_range_B_refined6.604
r_long_range_B_other6.429
r_dihedral_angle_1_deg6.109
r_scangle_other4.741
r_scbond_it3.079
r_scbond_other3.078
r_mcangle_it2.889
r_mcangle_other2.889
r_mcbond_it2.024
r_mcbond_other2.023
r_angle_refined_deg1.832
r_angle_other_deg0.9
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6452
Nucleic Acid Atoms
Solvent Atoms760
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction