3DGQ | pdb_00003dgq

Crystal structure of the glutathione transferase PI enzyme in complex with the bifunctional inhibitor, etharapta

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GSS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	100mM MES BUFFER PH 5.5, 22%(W/V) PEG 8000, 20mM CACL2, 10mM DTT, Small amounts of solid compound were streaked through the drops containing preformed crystals. These were soaked for 48hours., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.93	α = 90
b = 90.33	β = 98.88
c = 68.96	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++	ACXO	2006-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	1.6	19.53	98.3	0.046	0.046	13.2	3.6	62097	61004			21.56

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)
	1.6	1.69	96.1		0.554	0.554	1.3	3.5	8643

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		THROUGHOUT	5GSS	1.6	19.53	61004	3095	98.24	0.196	0.195	0.19	0.227	0.22	RANDOM	18.15

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]
0.77		-0.37	-0.51		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.947
r_dihedral_angle_4_deg	16.323
r_dihedral_angle_3_deg	11.145
r_dihedral_angle_1_deg	5.945
r_scangle_it	3.231
r_scbond_it	2.206
r_angle_refined_deg	1.539
r_mcangle_it	1.385
r_mcbond_it	0.979
r_nbtor_refined	0.312
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.155
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.128
r_metal_ion_refined	0.116
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3277
Nucleic Acid Atoms
Solvent Atoms	506
Heterogen Atoms	51

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction