9DGB | pdb_00009dgb

Tetrahydroprotoberberine N-methyltransferase in complex with (S)-reticuline 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	6.75	293	15 mM ammonium sulfate, 26% pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M Tris-Cl, 0.5 mM (S)-reticuline, 0.5 mM SAM, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.033	α = 90
b = 104.033	β = 90
c = 82.704	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	37.582	99.85	0.013	1	18.47	13.5		68219

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	97.12		0.724	0.451	0.85	13.6

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	37.582	68219	3492	99.845	0.176	0.1748	0.1803	0.1962	0.2	49.043

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]
0.027	0.013		0.027		-0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	10.951
r_lrange_it	10.87
r_dihedral_angle_3_deg	10.848
r_scangle_it	8.87
r_scbond_it	5.887
r_dihedral_angle_1_deg	5.534
r_mcangle_it	5.069
r_mcbond_it	3.619
r_dihedral_angle_2_deg	2.384
r_angle_refined_deg	1.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	10.951
r_lrange_it	10.87
r_dihedral_angle_3_deg	10.848
r_scangle_it	8.87
r_scbond_it	5.887
r_dihedral_angle_1_deg	5.534
r_mcangle_it	5.069
r_mcbond_it	3.619
r_dihedral_angle_2_deg	2.384
r_angle_refined_deg	1.004
r_nbtor_refined	0.298
r_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.189
r_symmetry_nbd_refined	0.16
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.081
r_gen_planes_refined	0.004
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2704
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	57

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.