4NHZ | pdb_00004nhz

Crystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290, with one glutathione bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MF7	PDB ENTRY 4MF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG4000, 0.1M TRIS-HCl pH 8.5, 0.2M calcium acetate, 5 mM GSH, cryoprotectant: 20% glycerol, vapor diffusion, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.998	α = 89.98
b = 99.359	β = 89.97
c = 108.734	γ = 89.99

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 QUANTUM 315	MIRRORS	2013-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	50	97.2	0.047	8.8	2		309970		-5

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	1.9	1.93	95.1		0.35	2.5	2

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 4MF7	1.901	50	303683	6282	97.03	0.18658	0.18577	0.1989	0.22542	0.236	RANDOM	31.684

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]
5.43	0.21	0.05	-2.95	0.06	-2.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.669
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_4_deg	12.236
r_long_range_B_other	10.659
r_long_range_B_refined	10.639
r_scangle_other	10.173
r_scbond_it	9.518
r_scbond_other	9.512
r_mcangle_other	5.65
r_mcangle_it	5.649
r_dihedral_angle_1_deg	5.502
r_mcbond_it	5.16
r_mcbond_other	5.157
r_angle_refined_deg	1.381
r_angle_other_deg	0.811
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29909
Nucleic Acid Atoms
Solvent Atoms	2214
Heterogen Atoms	314

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling