3HKP

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5296PEG 400 38%, MgCl2 0.1 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
1.9837.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.42α = 90
b = 37.39β = 96.28
c = 74.1γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANEL2008-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.992SOLEILPROXIMA 1

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
11.8573.7299.90.08411.23.72087218.9
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)
1.851.951000.4583.83.73014

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 REPLACEMENTTHROUGHOUTpdb entry 3HGI1.8534.419646106399.140.197250.194030.25825RANDOM19.303
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]
0.540.490.71-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.811
r_dihedral_angle_4_deg22.956
r_dihedral_angle_3_deg16.391
r_dihedral_angle_1_deg6.326
r_scangle_it4.064
r_scbond_it2.695
r_angle_refined_deg1.716
r_mcangle_it1.696
r_mcbond_it1.081
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.811
r_dihedral_angle_4_deg22.956
r_dihedral_angle_3_deg16.391
r_dihedral_angle_1_deg6.326
r_scangle_it4.064
r_scbond_it2.695
r_angle_refined_deg1.716
r_mcangle_it1.696
r_mcbond_it1.081
r_nbtor_refined0.313
r_symmetry_hbond_refined0.276
r_symmetry_vdw_refined0.251
r_nbd_refined0.225
r_xyhbond_nbd_refined0.19
r_chiral_restr0.148
r_metal_ion_refined0.082
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2002
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms53

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling