4ZBD

Crystal structure of the glutathione transferase URE2P6 from Phanerochaete chrysosporium in complex with glutathione reduced by X-ray irradiation at 100K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		278	30 % PEG4000, 10mM TRIS pH8.5, 0.2M Sodium Acetate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.455	α = 90
b = 50.096	β = 96.03
c = 97.141	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315r		2013-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.999	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.1	48.3	95.9	0.067	0.073	16.4	5.5		198807

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	1.1	1.2	90.9		0.157	0.16	6.7	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ZB8	1.12	26.646	1.37	165517	8324	96.58	0.1184	0.1171	0.1441

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	14.059
f_angle_d	1.5
f_chiral_restr	0.091
f_bond_d	0.01
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3582
Nucleic Acid Atoms
Solvent Atoms	698
Heterogen Atoms	80

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
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.