5O9W

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O7Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.4	277	19% PEG 3350, 200 mM disodium 2-oxoglutarate. Concentration of protein 37.5 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	130	CCD	AGILENT ATLAS CCD		2016-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	Agilent SuperNova	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	41.43	99	0.07	15.773	3.4		33795		-3	20.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	95		0.355	2.271	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5O7Y	1.85	41.43	31662	1633	97.57	0.16428	0.16175	0.21358	RANDOM	24.612

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]
-0.29			0.09		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.451
r_dihedral_angle_4_deg	16.878
r_dihedral_angle_3_deg	12.019
r_dihedral_angle_1_deg	6.283
r_long_range_B_refined	5.429
r_long_range_B_other	5.429
r_mcangle_other	3.018
r_mcangle_it	3.017
r_scangle_other	2.82
r_scbond_it	1.813
r_scbond_other	1.809
r_mcbond_it	1.799
r_mcbond_other	1.796
r_angle_refined_deg	1.414
r_angle_other_deg	0.911
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	2766
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	77

Software

Software
Software Name	Purpose
HKL-3000	phasing
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
REFMAC	refinement