3OJK

Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase in complex with 4-nitrocatechol at 1.68 Ang resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IG9PDB entry 2IG9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529313% PEG6000, 0.1 M calcium chloride, 0.1 M Tris-HCl. Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.102α = 90
b = 150.395β = 90
c = 95.941γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9801SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.6841.1997.20.05310.65.8180226175180318.8
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)
1.681.7791.70.3460.7422.14.823848

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 2IG91.6837.96166376869696.670.154430.1530.18153RANDOM20.873
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]
-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.183
r_dihedral_angle_4_deg18.926
r_dihedral_angle_3_deg12.729
r_dihedral_angle_1_deg7.023
r_scangle_it3.113
r_scbond_it2.015
r_angle_refined_deg1.46
r_mcangle_it1.147
r_angle_other_deg0.911
r_mcbond_it0.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.183
r_dihedral_angle_4_deg18.926
r_dihedral_angle_3_deg12.729
r_dihedral_angle_1_deg7.023
r_scangle_it3.113
r_scbond_it2.015
r_angle_refined_deg1.46
r_mcangle_it1.147
r_angle_other_deg0.911
r_mcbond_it0.696
r_mcbond_other0.239
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11512
Nucleic Acid Atoms
Solvent Atoms1369
Heterogen Atoms176

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling