3HJQ

Crystal structure of catechol 1,2-dioxygenase from Rhodococcus opacus 1CP in complex with 3-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
2.0339.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.938α = 90
b = 37.585β = 94.96
c = 74.81γ = 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
1244.77940.0980.098102.815870
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)
22.1190.90.5150.5152.72.72208

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 3HGI2201504681393.690.229360.226850.27349RANDOM28.939
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]
1.711.41-0.45-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg22.881
r_dihedral_angle_3_deg16.504
r_dihedral_angle_1_deg6.368
r_scangle_it3.772
r_scbond_it2.488
r_angle_refined_deg1.669
r_mcangle_it1.483
r_mcbond_it0.852
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg22.881
r_dihedral_angle_3_deg16.504
r_dihedral_angle_1_deg6.368
r_scangle_it3.772
r_scbond_it2.488
r_angle_refined_deg1.669
r_mcangle_it1.483
r_mcbond_it0.852
r_chiral_restr0.117
r_bond_refined_d0.017
r_gen_planes_refined0.009
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 Atoms2002
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms51

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling