5OES

The structure of a glutathione synthetase (StGSS1) from Solanum tuberosum in ADP and y-EC bound closed conformation.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1.4 M D-malic acid with the addition of 2.5 mM y-EC, 2.5 mM ADP, 5 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.39	α = 90
b = 154.39	β = 90
c = 344.325	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS3 6M		2015-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.98	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.48	50	99.8	0.145	0.154	12	8.9		143724

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54			1.238	1.309

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3KAL	2.48	50	140946	7240	99.96	0.2249	0.2241	0.2414	RANDOM	49.843

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]
2.5			2.5		-4.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.652
r_dihedral_angle_4_deg	17.107
r_dihedral_angle_3_deg	14.588
r_dihedral_angle_1_deg	6.031
r_angle_refined_deg	1.389
r_angle_other_deg	0.922
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.652
r_dihedral_angle_4_deg	17.107
r_dihedral_angle_3_deg	14.588
r_dihedral_angle_1_deg	6.031
r_angle_refined_deg	1.389
r_angle_other_deg	0.922
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21465
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms	268

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data processing
MOLREP	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.