3HJ8

Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol


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% PEG400, 0.1M Hepes, 0.1M magnesium chloride, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.1141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.572α = 90
b = 37.501β = 95.03
c = 74.917γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCD2007-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.542

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
12.372087.70.0521.162.039161
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)
2.372.479.50.1972.571.37

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 3HGI2.420875240088.20.1990.1950.288RANDOM34.85
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]
0.691.160.81-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.411
r_dihedral_angle_4_deg25.169
r_dihedral_angle_3_deg15.856
r_dihedral_angle_1_deg5.907
r_scangle_it2.067
r_scbond_it1.277
r_angle_refined_deg1.275
r_mcangle_it0.954
r_mcbond_it0.521
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.411
r_dihedral_angle_4_deg25.169
r_dihedral_angle_3_deg15.856
r_dihedral_angle_1_deg5.907
r_scangle_it2.067
r_scbond_it1.277
r_angle_refined_deg1.275
r_mcangle_it0.954
r_mcbond_it0.521
r_nbtor_refined0.306
r_symmetry_vdw_refined0.225
r_nbd_refined0.2
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.178
r_chiral_restr0.092
r_metal_ion_refined0.043
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1991
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms51

Software

Software
Software NamePurpose
CrysalisProdata collection
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling