2J5S

Structural of ABDH, a beta-diketone hydrolase from the Cyanobacterium Anabaena sp. PCC 7120 bound to (S)-3-oxocyclohexyl acetic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350, 0.2 M SODIUM MALONATE, 0.01 M BICYCLO[2.2.2]OCTANE-2,6-DIONE
Crystal Properties
Matthews coefficientSolvent content
2.0439.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.387α = 90
b = 80.387β = 90
c = 125.882γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.5740.1998.90.0632.0410.164435
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)
11.571.6389.90.272.934.8

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 1O8U1.5740.1960411322898.80.140.1380.17RANDOM14.19
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]
0.490.250.49-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.768
r_dihedral_angle_4_deg14.64
r_dihedral_angle_3_deg11.806
r_dihedral_angle_1_deg5.986
r_scangle_it2.542
r_scbond_it1.755
r_angle_refined_deg1.518
r_mcangle_it1.146
r_mcbond_it0.792
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.768
r_dihedral_angle_4_deg14.64
r_dihedral_angle_3_deg11.806
r_dihedral_angle_1_deg5.986
r_scangle_it2.542
r_scbond_it1.755
r_angle_refined_deg1.518
r_mcangle_it1.146
r_mcbond_it0.792
r_nbtor_refined0.317
r_nbd_refined0.226
r_symmetry_vdw_refined0.171
r_symmetry_hbond_refined0.156
r_xyhbond_nbd_refined0.134
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms4016
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing