3HHY

Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with catechol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529639% PEG400, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.0138.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.829α = 90
b = 37.482β = 95.73
c = 74.479γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.000ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.5544.32499.80.07411.83.43382222.215
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.551.6399.90.55122.914728

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 REPLACEMENTTHROUGHOUT3HGI1.552033822177999.630.210080.208460.239RANDOM27.015
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]
0.90.51-0.07-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.13
r_dihedral_angle_4_deg24.892
r_dihedral_angle_3_deg14.657
r_dihedral_angle_1_deg5.896
r_scangle_it3.269
r_scbond_it2.26
r_mcangle_it1.536
r_angle_refined_deg1.534
r_mcbond_it0.967
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.13
r_dihedral_angle_4_deg24.892
r_dihedral_angle_3_deg14.657
r_dihedral_angle_1_deg5.896
r_scangle_it3.269
r_scbond_it2.26
r_mcangle_it1.536
r_angle_refined_deg1.534
r_mcbond_it0.967
r_nbtor_refined0.317
r_nbd_refined0.214
r_symmetry_hbond_refined0.214
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.178
r_chiral_restr0.127
r_metal_ion_refined0.059
r_symmetry_metal_ion_refined0.051
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2002
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms70

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling