8IHG

Crystal structure of aminophenol dioxygenase from Pseudomonas species AP-3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VSG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289magnesium chloride hexahydrate, 0.1 M TRIS pH 8.5, 21% v/v polyethylene glycol 8000
Crystal Properties
Matthews coefficientSolvent content
4.0669.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.475α = 90
b = 153.475β = 90
c = 312.036γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2022-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9791SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.85881.9121000.995122051097
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.863.010.872

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.85881.9121.3450991200099.920.18110.17890.2337
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
f_dihedral_angle_d3.688
f_angle_d1.062
f_chiral_restr0.058
f_bond_d0.009
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8891
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms30

Software

Software
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing