3HJS

Crystal structure of catechol 1,2-dioxygenase from Rhodococcus opacus 1CP in complex with 4-methylcatechol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529639% PEG 400, 0.1 M Hepes, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
1.9938.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.2α = 90
b = 37.363β = 95.82
c = 74.702γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.874.399.80.0850.08512.23.522751
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.91000.2340.2343.63.13317

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 3HGI1.82021564116499.740.205240.202470.25507RANDOM24.448
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]
1.150.16-0.44-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.993
r_dihedral_angle_4_deg21.416
r_dihedral_angle_3_deg12.319
r_dihedral_angle_1_deg5.896
r_scangle_it4.675
r_scbond_it2.982
r_mcangle_it1.843
r_angle_refined_deg1.632
r_mcbond_it1.066
r_chiral_restr0.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.993
r_dihedral_angle_4_deg21.416
r_dihedral_angle_3_deg12.319
r_dihedral_angle_1_deg5.896
r_scangle_it4.675
r_scbond_it2.982
r_mcangle_it1.843
r_angle_refined_deg1.632
r_mcbond_it1.066
r_chiral_restr0.121
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1988
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms52

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling