9DGA | pdb_00009dga

Tetrahydroprotoberberine N-methyltransferase in complex with (R)-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	6.5	293	0.1 M Tris-Cl, 15 mM ammonium sulfate, 29% pentaerythritol ethoxylate (15/4 EO/OH), 5% glycerol, 0.5 mM SAM, 0.5 mM R-reticuline

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.013	α = 90
b = 104.013	β = 90
c = 82.863	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		2020-07-03	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	2	37.641	98.36	0.044	0.996	10.31	3.4		34747

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	2	2.05	99.81		0.139	0.939	4.78	3.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	37.641	34747	1783	98.344	0.149	0.1463	0.1482	0.1906	0.1907	RANDOM	28.469

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]
0.061	0.031		0.061		-0.198

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	14.003
r_dihedral_angle_6_deg	12.291
r_dihedral_angle_3_deg	11.282
r_scangle_it	10.46
r_scbond_it	7.512
r_dihedral_angle_1_deg	5.923
r_mcangle_it	5.73
r_mcbond_it	4.618
r_dihedral_angle_2_deg	3.166
r_angle_refined_deg	1.379

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	14.003
r_dihedral_angle_6_deg	12.291
r_dihedral_angle_3_deg	11.282
r_scangle_it	10.46
r_scbond_it	7.512
r_dihedral_angle_1_deg	5.923
r_mcangle_it	5.73
r_mcbond_it	4.618
r_dihedral_angle_2_deg	3.166
r_angle_refined_deg	1.379
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.21
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.197
r_chiral_restr	0.096
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2696
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	51

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.