2VCV | pdb_00002vcv

Glutathione transferase A3-3 in complex with glutathione and delta-4- androstene-3-17-dione

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8		HANGING VAPOUR DROP TECHIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 25 MM ANDROSTENE DIONE.

Crystal Properties
Matthews coefficient	Solvent content
2.09	40.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.177	α = 89.76
b = 92.064	β = 89.72
c = 113.54	γ = 89.73

Symmetry
Space Group	P 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 CCD	SAGITALLY FOCUSING GE(220) AND A MULTILAYER	2006-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.8	20	94.9	0.07	8	1.9		338219		1.9	17.4

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	1.8	1.9	93.6		0.38	1.9	1.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TDI	1.8	20	304874	16208	94.9	0.225	0.223	0.22	0.267	0.27	RANDOM	20.44

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]
1.93	-0.03	-0.08	-1.13	0.23	-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.486
r_dihedral_angle_3_deg	15.642
r_dihedral_angle_4_deg	14.976
r_dihedral_angle_1_deg	5.2
r_scangle_it	2.008
r_angle_refined_deg	1.331
r_scbond_it	1.308
r_mcangle_it	0.835
r_mcbond_it	0.503
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28208
Nucleic Acid Atoms
Solvent Atoms	3263
Heterogen Atoms	551

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing