3I4V | pdb_00003i4v

Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 3-chlorocatechol


X-RAY DIFFRACTION

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
2.0941.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.655α = 90
b = 37.886β = 95.31
c = 75.26γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-07-24MSINGLE 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
1237.4887.20.1110.1116.22.215091
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)
22.1190.50.3950.3951.52.22284

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2201431076986.190.23880.23550.240.298380.3RANDOM41.995
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]
3.611.77-0.7-2.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.465
r_dihedral_angle_3_deg17.23
r_dihedral_angle_4_deg16.687
r_dihedral_angle_1_deg7.337
r_scangle_it3.079
r_scbond_it2.096
r_angle_refined_deg1.643
r_mcangle_it1.433
r_mcbond_it0.811
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.465
r_dihedral_angle_3_deg17.23
r_dihedral_angle_4_deg16.687
r_dihedral_angle_1_deg7.337
r_scangle_it3.079
r_scbond_it2.096
r_angle_refined_deg1.643
r_mcangle_it1.433
r_mcbond_it0.811
r_chiral_restr0.125
r_bond_refined_d0.015
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 Atoms93
Heterogen Atoms51

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling