4KVJ

Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.130045% PEG 400, 0.2M lithium chloride, 0.1M sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
3.160.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.279α = 90
b = 129.65β = 90
c = 187.711γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
12.129499.60.04717.84.45036650366-3-3
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)
12.122.231000.4612.64.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1293.865036647796256499.320.171740.169870.20788RANDOM44.203
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]
0.10.03-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_4_deg15.643
r_dihedral_angle_3_deg13.792
r_dihedral_angle_1_deg5.737
r_mcangle_it2.389
r_scbond_it1.826
r_mcbond_it1.485
r_mcbond_other1.485
r_angle_refined_deg1.15
r_angle_other_deg0.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_4_deg15.643
r_dihedral_angle_3_deg13.792
r_dihedral_angle_1_deg5.737
r_mcangle_it2.389
r_scbond_it1.826
r_mcbond_it1.485
r_mcbond_other1.485
r_angle_refined_deg1.15
r_angle_other_deg0.727
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4913
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms192

Software

Software
Software NamePurpose
JDirectordata collection
PHASERphasing
REFMACrefinement
autoPROCdata scaling
XDSdata reduction
SCALAdata scaling