3DSK

Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase variant (F137L) (At-AOS(F137L), Cytochrome P450 74A, CYP74A) Complexed with 12R,13S-Vernolic Acid at 1.55 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CLIPDB ENTRY 3CLI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293PEG4000, Glycerol, Tris-HCl, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.612α = 90
b = 105.463β = 90
c = 162.632γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2007-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9998SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5510098.9155392155392
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5897.6

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3CLI1.5588.39147287147287779198.330.183470.183470.182270.20633RANDOM20.579
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]
0.36-0.22-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.181
r_dihedral_angle_4_deg15.884
r_dihedral_angle_3_deg11.936
r_dihedral_angle_1_deg5.581
r_scangle_it3.212
r_scbond_it2.067
r_angle_refined_deg1.292
r_mcangle_it1.226
r_mcbond_it0.765
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.181
r_dihedral_angle_4_deg15.884
r_dihedral_angle_3_deg11.936
r_dihedral_angle_1_deg5.581
r_scangle_it3.212
r_scbond_it2.067
r_angle_refined_deg1.292
r_mcangle_it1.226
r_mcbond_it0.765
r_nbtor_refined0.307
r_nbd_refined0.205
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.124
r_xyhbond_nbd_refined0.118
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7420
Nucleic Acid Atoms
Solvent Atoms748
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing