3GX0 | pdb_00003gx0

Crystal Structure of GSH-dependent Disulfide bond Oxidoreductase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			Protein in 20 mM potassium dihydrogen phosphate, 2 mM DTT, 1mM EDTA, 10 mM glutathione. Well solution: 20% w/v PEG 3000, 100 mM acetate., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.49	α = 90
b = 68.49	β = 90
c = 111.99	γ = 90

Symmetry
Space Group	P 41 21 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	Bruker Platinum 135	Montel graded multilayer optics from Bruker Nonius	2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.3	20	99.8	0.13	17.5	10.9		12571

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)
	2.3	2.4	98.5		0.551	3.35	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	20	11342	584	96.26	0.1935	0.19068	0.1897	0.24981	0.2491	RANDOM	27.87

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]
-1.01			-1.01		2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.998
r_dihedral_angle_4_deg	16.945
r_dihedral_angle_3_deg	15.647
r_dihedral_angle_1_deg	6.691
r_scangle_it	3.427
r_scbond_it	2.24
r_angle_refined_deg	1.662
r_mcangle_it	1.594
r_mcbond_it	0.905
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.246
r_symmetry_hbond_refined	0.213
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.122
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1658
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SAINT	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction