6ZJC | pdb_00006zjc

Crystal structure of Equus ferus caballus glutathione transferase A3-3 in complex with glutathione and triethyltin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZJ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	0.1 M Bicine/Trizma base pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M of each monosaccharide (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, and N-acetyl-D-glucosamine), and 20 mM triethyltin bromide

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.401	α = 88.17
b = 54.728	β = 78.74
c = 97.115	γ = 86.39

Symmetry
Space Group	P 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 PILATUS3 6M		2020-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96852	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.2	48.37	98.4	0.119	0.141	0.075	0.992	6.4	3.5		49746

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	97.4		0.442	0.523	0.277	0.914		3.5

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6ZJ9	2.2	48.37	47212	2503	98.31	0.1751	0.1732	0.18	0.2095	0.22	RANDOM	32.704

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]
5.82	-1.17	2.72	-2.84	-0.47	-1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.474
r_dihedral_angle_4_deg	17.353
r_dihedral_angle_3_deg	15.286
r_dihedral_angle_1_deg	6.028
r_angle_other_deg	2.186
r_angle_refined_deg	1.654
r_chiral_restr	0.085
r_bond_other_d	0.033
r_bond_refined_d	0.012
r_gen_planes_other	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.474
r_dihedral_angle_4_deg	17.353
r_dihedral_angle_3_deg	15.286
r_dihedral_angle_1_deg	6.028
r_angle_other_deg	2.186
r_angle_refined_deg	1.654
r_chiral_restr	0.085
r_bond_other_d	0.033
r_bond_refined_d	0.012
r_gen_planes_other	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7076
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	140

Software

Software
Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction

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.