4P9G

Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop crystallisation trials. Well solution: 10 % w/v PEG 1k and 10 % PEG 10k (Molecular Dimensions Structure Screen 2, condition 46).
Crystal Properties
Matthews coefficientSolvent content
2.4856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.557α = 90
b = 82.557β = 90
c = 114.008γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2013-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.072ESRFBM14

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
12.25786.30.13612.69.810549
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.349.40.6193.17.1

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 REPLACEMENTTHROUGHOUT3ebr, 2oq1, 3bal, 3cjx2.271.51002151286.170.175640.173420.21758RANDOM29.697
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]
-0.7-0.35-0.71.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.018
r_dihedral_angle_3_deg19.201
r_dihedral_angle_4_deg18.956
r_dihedral_angle_1_deg7.77
r_angle_refined_deg2.008
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.018
r_dihedral_angle_3_deg19.201
r_dihedral_angle_4_deg18.956
r_dihedral_angle_1_deg7.77
r_angle_refined_deg2.008
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.011
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1234
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
BALBESphasing
MOLREPphasing
ARPmodel building