2PGN

The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729823% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1843.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.6α = 90
b = 123.6β = 90
c = 144.3γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

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
11.14084.80.06813.586.138886737904512.26
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)
11.11.249.90.4872.73.650802

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONknown crystal structureTHROUGHOUT1.2103338583338581659397.170.150.150.1490.176RANDOM12.78
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]
0.750.75-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.859
r_dihedral_angle_4_deg16.822
r_dihedral_angle_3_deg13.719
r_sphericity_free8.377
r_dihedral_angle_1_deg6.736
r_sphericity_bonded5.477
r_scangle_it4.005
r_scbond_it3.235
r_mcangle_it2.394
r_rigid_bond_restr2.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.859
r_dihedral_angle_4_deg16.822
r_dihedral_angle_3_deg13.719
r_sphericity_free8.377
r_dihedral_angle_1_deg6.736
r_sphericity_bonded5.477
r_scangle_it4.005
r_scbond_it3.235
r_mcangle_it2.394
r_rigid_bond_restr2.139
r_angle_refined_deg2.052
r_mcbond_it1.995
r_mcbond_other1.766
r_angle_other_deg1.391
r_symmetry_vdw_refined0.317
r_symmetry_vdw_other0.309
r_xyhbond_nbd_refined0.25
r_nbd_refined0.222
r_symmetry_hbond_refined0.212
r_nbd_other0.192
r_nbtor_refined0.171
r_chiral_restr0.128
r_nbtor_other0.084
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8886
Nucleic Acid Atoms
Solvent Atoms1268
Heterogen Atoms290

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction