5O9W

Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with 2-oxoglutarate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.427719% PEG 3350, 200 mM disodium 2-oxoglutarate. Concentration of protein 37.5 mg/ml.
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.044α = 90
b = 87.424β = 90
c = 94.863γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130CCDAGILENT ATLAS CCD2016-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEAgilent SuperNova1.54

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
11.8541.43990.0715.7733.433795-320.7
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)
11.851.88950.3552.2712.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5O7Y1.8541.4331662163397.570.164280.161750.21358RANDOM24.612
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]
-0.290.090.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.451
r_dihedral_angle_4_deg16.878
r_dihedral_angle_3_deg12.019
r_dihedral_angle_1_deg6.283
r_long_range_B_refined5.429
r_long_range_B_other5.429
r_mcangle_other3.018
r_mcangle_it3.017
r_scangle_other2.82
r_scbond_it1.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.451
r_dihedral_angle_4_deg16.878
r_dihedral_angle_3_deg12.019
r_dihedral_angle_1_deg6.283
r_long_range_B_refined5.429
r_long_range_B_other5.429
r_mcangle_other3.018
r_mcangle_it3.017
r_scangle_other2.82
r_scbond_it1.813
r_scbond_other1.809
r_mcbond_it1.799
r_mcbond_other1.796
r_angle_refined_deg1.414
r_angle_other_deg0.911
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms2766
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms77

Software

Software
Software NamePurpose
HKL-3000phasing
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMACrefinement