6VD1 | pdb_00006vd1

Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with S-adenosylmethionine and PPNP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	0.12 M Alcohols (1,6-hexanediol; 1-butanol; 1,2-propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol), 0.1 M HEPES and MOPS buffer at pH 7.5, 20% mmPEG500, 10% PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.205	α = 90
b = 101.484	β = 99.37
c = 84.334	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2018-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	1.32	47.09	97.8	0.056	12.45	3.35		232535		-3

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	1.32	1.4	98.2		0.585	2.03	3.35

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6VCZ	1.32	47.09	231370	1163	97.83	0.1418	0.1416	0.1732	RANDOM	15.039

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]
2.67		0.57	-1.45		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.051
r_dihedral_angle_3_deg	12.487
r_dihedral_angle_4_deg	11.829
r_dihedral_angle_1_deg	6.646
r_rigid_bond_restr	2.736
r_angle_refined_deg	1.81
r_angle_other_deg	1.542
r_chiral_restr	0.109
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.051
r_dihedral_angle_3_deg	12.487
r_dihedral_angle_4_deg	11.829
r_dihedral_angle_1_deg	6.646
r_rigid_bond_restr	2.736
r_angle_refined_deg	1.81
r_angle_other_deg	1.542
r_chiral_restr	0.109
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6088
Nucleic Acid Atoms
Solvent Atoms	1220
Heterogen Atoms	191

Software

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

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.