9DG9 | pdb_00009dg9

Tetrahydroprotoberberine N-methyltransferase E207A mutant 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	26% Pentaerythritol ethoxylate (15/4 EO/OH), 15 mM ammonium sulfate, 6% Glycerol, 0.5 mM (R)-reticuline, 0.5 mM SAM, 0.1 mM Tris-Cl

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.693	α = 90
b = 103.693	β = 90
c = 82.697	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	39.46	99.81	0.016	1	14.84	13.4		67813

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	100		0.44	0.698	1.14	13.7

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	39.459	67813	3468	99.863	0.179	0.1777	0.181	0.1958	0.1965	43.702

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]
0.019	0.009		0.019		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.537
r_lrange_it	11.591
r_dihedral_angle_3_deg	11.062
r_scangle_it	9.066
r_scbond_it	6.584
r_dihedral_angle_1_deg	5.833
r_mcangle_it	4.998
r_mcbond_it	3.913
r_dihedral_angle_2_deg	2.564
r_angle_refined_deg	1.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.537
r_lrange_it	11.591
r_dihedral_angle_3_deg	11.062
r_scangle_it	9.066
r_scbond_it	6.584
r_dihedral_angle_1_deg	5.833
r_mcangle_it	4.998
r_mcbond_it	3.913
r_dihedral_angle_2_deg	2.564
r_angle_refined_deg	1.165
r_nbtor_refined	0.303
r_symmetry_nbd_refined	0.209
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.159
r_chiral_restr	0.087
r_gen_planes_refined	0.005
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2693
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	63

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.