2OG6

Crystal structure of asparagine oxygenase in complex with Fe(II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DRY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62912.5 M sodium acetate, 0.1 M Hepes, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7455.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.733α = 90
b = 90.733β = 90
c = 89.791γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.5418

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
11.92098.60.0738.37.743361026008330.6
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)
11.91.9378.80.4162.11331

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1DRY1.916203322132988103399.290.2320.170.1690.197RANDOM34.046
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]
0.350.170.35-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.27
r_dihedral_angle_4_deg18.55
r_dihedral_angle_3_deg11.267
r_dihedral_angle_1_deg6.064
r_scangle_it2.084
r_scbond_it1.352
r_angle_refined_deg1.193
r_angle_other_deg0.897
r_mcangle_it0.887
r_mcbond_it0.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.27
r_dihedral_angle_4_deg18.55
r_dihedral_angle_3_deg11.267
r_dihedral_angle_1_deg6.064
r_scangle_it2.084
r_scbond_it1.352
r_angle_refined_deg1.193
r_angle_other_deg0.897
r_mcangle_it0.887
r_mcbond_it0.811
r_symmetry_vdw_other0.31
r_nbd_refined0.207
r_nbd_other0.2
r_nbtor_refined0.166
r_symmetry_vdw_refined0.164
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.102
r_mcbond_other0.101
r_nbtor_other0.083
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2477
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing