2Q0L | pdb_00002q0l

Helicobacter pylori thioredoxin reductase reduced by sodium dithionite 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
2.4	48.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.451	α = 90
b = 99.455	β = 97.94
c = 64.765	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	1.45	64.15	94.5	0.057	0.057	5.2	3.5	105645	105645			14.5

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	1.45	1.53	69.7		0.19	0.19	3.6	2.8	11370

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.45	64.15	105611	105611	5277	94.48	0.168	0.168	0.167	0.18	0.193	0.2	RANDOM	12.621

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]
0.06		0.07	0.17		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.878
r_dihedral_angle_4_deg	18.87
r_dihedral_angle_3_deg	11.721
r_dihedral_angle_1_deg	5.064
r_sphericity_free	4.177
r_scangle_it	2.79
r_scbond_it	2.169
r_sphericity_bonded	1.94
r_angle_refined_deg	1.495
r_mcangle_it	1.433
r_mcbond_it	1.224
r_rigid_bond_restr	1.155
r_angle_other_deg	0.828
r_mcbond_other	0.335
r_nbd_refined	0.205
r_chiral_restr	0.204
r_nbd_other	0.191
r_nbtor_refined	0.181
r_symmetry_vdw_other	0.143
r_symmetry_vdw_refined	0.12
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.09
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.017
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4708
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	202

Software

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