6D0O | pdb_00006d0o

rdpA dioxygenase holoenzyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5294The protein solution was 10-20 mg/ml in 20mM Tris-pH 8, 50mM NaCl, 5mM bME. The precipitant solution was 0.1M Hepes-pH 7.5, 10(w/v)% PEG 8K, 8(v/v)% ethylene glycol.
Crystal Properties
Matthews coefficientSolvent content
3.4564.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.014α = 90
b = 153.014β = 90
c = 156.845γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3109.61000.11323.56.979857
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341000.7616.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.35076047379399.880.187820.185860.190.228430.23RANDOM45.479
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]
0.390.39-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.892
r_dihedral_angle_4_deg19.682
r_dihedral_angle_3_deg18.328
r_long_range_B_refined10.331
r_long_range_B_other10.325
r_dihedral_angle_1_deg7.747
r_scangle_other7.65
r_mcangle_other7.023
r_mcangle_it7.021
r_scbond_it5.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.892
r_dihedral_angle_4_deg19.682
r_dihedral_angle_3_deg18.328
r_long_range_B_refined10.331
r_long_range_B_other10.325
r_dihedral_angle_1_deg7.747
r_scangle_other7.65
r_mcangle_other7.023
r_mcangle_it7.021
r_scbond_it5.265
r_scbond_other5.224
r_mcbond_it4.81
r_mcbond_other4.779
r_angle_refined_deg1.975
r_angle_other_deg1.212
r_chiral_restr0.172
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8891
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing