3ISH

Crystal structure of Helicobacter pylori thioredoxin reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A87	PDB ENTRY 2A87

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	277	2.0 M Ammonium sulfate,0.2M Ammonium Nitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.4	α = 90
b = 89.4	β = 90
c = 279.9	γ = 120

Symmetry
Space Group	P 32 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 225 mm CCD	MIRRORS	2007-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1

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	2.43	19.98		0.068	0.068	24.31	10.5		49803		-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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2A87	2.43	19.98	47307	2490	100	0.181	0.178	0.252	RANDOM	39.07

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.265
r_dihedral_angle_4_deg	24.348
r_dihedral_angle_3_deg	21.942
r_dihedral_angle_1_deg	7.217
r_scangle_it	5.346
r_scbond_it	3.401
r_angle_refined_deg	2.402
r_mcangle_it	2.063
r_mcbond_it	1.246
r_nbtor_refined	0.317
r_nbd_refined	0.263
r_symmetry_hbond_refined	0.248
r_xyhbond_nbd_refined	0.232
r_symmetry_vdw_refined	0.223
r_chiral_restr	0.189
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
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	7061
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	159

Software

Software
Software Name	Purpose
XDS	data scaling
MrBUMP	phasing
REFMAC	refinement
XDS	data reduction