3DD3 | pdb_00003dd3

Crystal Structure of the Glutathione Transferase Pi enzyme in complex with the bifunctional inhibitor, Etharapta

X-RAY DIFFRACTION

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 or 6.0, 22%(w/v) PEG 8000, 20mM CaCl2, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.69	α = 90
b = 89.54	β = 97.81
c = 68.99	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	MARMOSAIC 300 mm CCD	mirrors	2007-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.77	APS	23-ID-B

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	2.25	68.36	99.5	0.1	0.1	4.3	3.6	21983	21865			36.96

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	2.25	2.37	96.6		0.56	0.56	1	3	3071

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	5GSS	2.25	68.36	21862	20718	1144	99.45	0.24	0.2	0.2	0.2	0.26	0.27	RANDOM	43.88

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]
6.61		-0.66	-2.9		-3.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.697
r_dihedral_angle_4_deg	16.664
r_dihedral_angle_3_deg	15.919
r_dihedral_angle_1_deg	6.052
r_scangle_it	3.479
r_scbond_it	2.28
r_angle_refined_deg	1.606
r_mcangle_it	1.542
r_mcbond_it	0.927
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.697
r_dihedral_angle_4_deg	16.664
r_dihedral_angle_3_deg	15.919
r_dihedral_angle_1_deg	6.052
r_scangle_it	3.479
r_scbond_it	2.28
r_angle_refined_deg	1.606
r_mcangle_it	1.542
r_mcbond_it	0.927
r_nbtor_refined	0.311
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.173
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3277
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	71

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
REFMAC	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.