6VCZ | pdb_00006vcz

Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2)

X-RAY DIFFRACTION

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Starting Model(s)

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

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	57.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.798	α = 90
b = 99.276	β = 109.74
c = 86.93	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	CCD	RAYONIX MX300-HS		2018-11-01	M	SINGLE WAVELENGTH

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

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	1.52	42.44	99.7	0.054	16.26	4.12		154106		-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	1.52	1.61	99.3		0.609	2.15	3.96

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	6VCW	1.52	42.44	152562	1542	99.82	0.1605	0.1603	0.1799	RANDOM	20.307

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]
-0.32		0.35	-0.31		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.563
r_dihedral_angle_1_deg	18.989
r_dihedral_angle_4_deg	15.124
r_dihedral_angle_3_deg	13.37
r_angle_refined_deg	2.003
r_angle_other_deg	1.552
r_chiral_restr	0.111
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5868
Nucleic Acid Atoms
Solvent Atoms	1024
Heterogen Atoms	95

Software

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