1XWK | pdb_00001xwk

2.3 angstrom resolution crystal structure of human glutathione S-transferase M1A-1A complexed with glutathionyl-S-dinitrobenzene

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GTU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	280	20% PEG4000, pH 6.00, VAPOR DIFFUSION, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.83	α = 90
b = 51.94	β = 121.08
c = 93.84	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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2001-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.3	20	83.7	0.06	0.051	10.8	15.4	32953	27431			17.1

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)
	2.3	2.38	47.2		0.269	0.302	2.3	3.7	1528

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1GTU	2.3	20	1	27431	26990	822	82.7	0.256	0.243	0.243	0.23	0.281	0.26	RANDOM	55.6

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]
-10.75		-5.06	20.04		-9.29

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.4
c_scangle_it	7
c_mcangle_it	4.89
c_scbond_it	4.11
c_mcbond_it	2.72
c_angle_deg	1.2
c_improper_angle_d	1.12
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5412
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
CCP4	model building
CNS	refinement
CCP4	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.