1ULJ

Biphenyl dioxygenase (BphA1A2) in complex with the substrate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 4000, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.754.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.834α = 90
b = 137.834β = 90
c = 237.96γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.978Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.63899.30.1010.1016.75.7703357033541.6
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)
12.62.7498.40.3570.3572.15.710013

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.636.767104169840352298.310.186050.186050.183520.23361RANDOM28.852
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.761
r_scangle_it2.083
r_angle_refined_deg1.257
r_scbond_it1.214
r_mcangle_it0.964
r_angle_other_deg0.811
r_mcbond_it0.512
r_symmetry_vdw_other0.26
r_nbd_other0.232
r_nbd_refined0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.761
r_scangle_it2.083
r_angle_refined_deg1.257
r_scbond_it1.214
r_mcangle_it0.964
r_angle_other_deg0.811
r_mcbond_it0.512
r_symmetry_vdw_other0.26
r_nbd_other0.232
r_nbd_refined0.183
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.141
r_symmetry_vdw_refined0.126
r_metal_ion_refined0.096
r_nbtor_other0.082
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14586
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing