2PVQ | pdb_00002pvq

Crystal structure of Ochrobactrum anthropi glutathione transferase Cys10Ala mutant with glutathione bound at the H-site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NTO	PDB ENTRY 2NTO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	2.0 M ammonium sulfate, 100 mM Tris-HCl, 200 mM Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.373	α = 90
b = 58.373	β = 90
c = 214.023	γ = 120

Symmetry
Space Group	P 61 2 2

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		2006-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.934	ESRF	ID23-1

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	1.803	50.64	99.8	0.085	16	66.6	20967	20967	2	1	23.056

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	1.803	1.86	100		0.401	3.51	8.2	2032

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2NTO	1.803	50.64	2	20967	19866	1074	99.87	0.20006	0.19762	0.21	0.24772	0.26	RANDOM	25.56

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]
1.77	0.89		1.77		-2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.117
r_scangle_it	2.899
r_scbond_it	1.862
r_angle_refined_deg	1.303
r_mcangle_it	1.093
r_angle_other_deg	0.807
r_mcbond_it	0.662
r_symmetry_vdw_other	0.333
r_nbd_other	0.25
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.19
r_symmetry_hbond_refined	0.147
r_nbtor_other	0.086
r_chiral_restr	0.074
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1534
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	30

Software

Software
Software Name	Purpose
ADSC	data collection
FFT	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
FFT	phasing