9DGE | pdb_00009dge

Tetrahydroprotoberberine N-methyltransferase product complex with dextromethorphan and SAM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6P3O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	26% pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M Tris-Cl, 10 mM ammonium sulfate, 5% glycerol, 0.5 mM dextromethorphan, 0.5 mM SAM

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.992	α = 90
b = 103.992	β = 90
c = 82.536	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2020-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	1.6	39.53	99.88	0.011	1	19.52	13.4		68044

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.62	99.7		0.312	0.791	1.98	13.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	39.53	68043	3480	99.877	0.172	0.1707	0.176	0.1912	0.1942	38.517

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]
0.088	0.044		0.088		-0.285

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.703
r_dihedral_angle_3_deg	11.37
r_lrange_it	10.291
r_scangle_it	8.356
r_scbond_it	5.771
r_dihedral_angle_1_deg	5.763
r_mcangle_it	5.059
r_mcbond_it	3.578
r_dihedral_angle_2_deg	2.817
r_angle_refined_deg	1.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.703
r_dihedral_angle_3_deg	11.37
r_lrange_it	10.291
r_scangle_it	8.356
r_scbond_it	5.771
r_dihedral_angle_1_deg	5.763
r_mcangle_it	5.059
r_mcbond_it	3.578
r_dihedral_angle_2_deg	2.817
r_angle_refined_deg	1.117
r_nbtor_refined	0.302
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.19
r_symmetry_nbd_refined	0.186
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.089
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2721
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.