5HFK | pdb_00005hfk

CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE PROTEIN FROM ESCHERICHIA COLI OCh 157:H7 STR. SAKAI (ECs3186, TARGET EFI-507414) WITH BOUND GLUTATHIONE

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	6.5	298	Protein (18.49 mg/ml, 20 mM HEPES pH 7.5, 0.150 M Sodium Chloride, 5% v/v Glycerol, 4.5 mM DTT, 5 mM reduced Glutathione) were combined with an equal volume of Reservoir (100 mM Bis-tris pH 6.5, 100 mM Magnesium Chloride, 2.8 M Sodium Chloride); Cryoprotection (Equal volumes of Reservoir + 50% v/v Glycerol)

Crystal Properties
Matthews coefficient	Solvent content
2.75	59.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.267	α = 90
b = 83.267	β = 90
c = 171.153	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	CCD	RAYONIX MX225HE	MIRRORS	2014-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	1.55	20	98.2	0.093	11.6	7.1		86041			16.72

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	1.55	1.61	92.5		0.421	2.653	3.3	7961

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3GX0	1.551	19.655	1.45	85985	4282	98.03	0.1868	0.1855	0.19	0.2125	0.21	24.4518

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	14.005
f_angle_d	1.188
f_chiral_restr	0.07
f_bond_d	0.01
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3324
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms	80

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data reduction
SCALEPACK	data scaling
PHASES	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.