2Q0K

Oxidized thioredoxin reductase from Helicobacter pylori in complex with NADP+

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	22% PEG 3350, 0.1M MIB pH 6.0, 8mM pentaethylene glycol monooctyl ether, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.128	α = 90
b = 99.195	β = 100.02
c = 64.436	γ = 90

Symmetry
Space Group	P 1 21 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		2006-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9393	ESRF	ID23-1

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	1.7	63.5	98.4	0.059	0.059	5.4	3.5	66999	66999

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	90.2		0.429	0.429	1.7	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1TDE	1.7	63.5	66969	63605	3364	98.32	0.19024	0.18834	0.22605	RANDOM	23.304

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]
0.79		0.91	-2.18		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.254
r_dihedral_angle_4_deg	19.184
r_dihedral_angle_3_deg	13.722
r_dihedral_angle_1_deg	5.378
r_scangle_it	2.306
r_scbond_it	1.746
r_angle_refined_deg	1.604
r_mcangle_it	0.984
r_angle_other_deg	0.858
r_mcbond_it	0.814
r_symmetry_vdw_refined	0.23
r_mcbond_other	0.226
r_nbd_refined	0.206
r_nbd_other	0.194
r_symmetry_hbond_refined	0.193
r_symmetry_vdw_other	0.186
r_nbtor_refined	0.181
r_chiral_restr	0.165
r_xyhbond_nbd_refined	0.132
r_nbtor_other	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4688
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	202

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
REFMAC	phasing