4IVF | pdb_00004ivf

Crystal structure of glutathione transferase homolog from Lodderomyces elongisporus, target EFI-501753, with two GSH per subunit

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	298	Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.17M Amm Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5% Peg4000, 15% (V/V) glycerol); Cryoprotection (Reservoir taken to 20% glycerol), vapor diffusion, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.598	α = 90
b = 112.476	β = 90
c = 194.384	γ = 90

Symmetry
Space Group	P 21 21 21

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 MX225HE	MIRRORS	2012-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	194.384	98.5	0.175	7.1	6.1	99618	99618

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	97.9		0.7	0.7	1.1	6.1	14286

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3GX0	2.2	37.126	99532	99532	4984	98.2	0.1592	0.1559	0.16	0.2234	0.22	RANDOM	24.4895

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.636
f_angle_d	1.018
f_chiral_restr	0.075
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14481
Nucleic Acid Atoms
Solvent Atoms	1271
Heterogen Atoms	333

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BALBES	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.