7V25

Crystal Structure of phthalate dioxygenase in complex with phthalate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293PEG4000, calcium chloride, magnesium chloride, sodium potassium tartrate
Crystal Properties
Matthews coefficientSolvent content
3.1260.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.03α = 90
b = 122.18β = 101.13
c = 162.94γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

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
12.74159.8898.10.99512.61.988962
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)
12.742.790.805

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 REPLACEMENTTHROUGHOUT7FHR2.74159.8884574438898.030.21040.20670.2826RANDOM50.688
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]
-0.16-0.030.17-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.39
r_dihedral_angle_3_deg18.315
r_dihedral_angle_4_deg17.982
r_dihedral_angle_1_deg8.124
r_angle_refined_deg1.409
r_chiral_restr0.109
r_gen_planes_refined0.006
r_bond_refined_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19274
Nucleic Acid Atoms
Solvent Atoms1229
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing