3D8X

Crystal Structure of Saccharomyces cerevisiae NDPPH Dependent Thioredoxin Reductase 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	291	pH 6.5, EVAPORATION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.229	α = 90
b = 125.004	β = 114.16
c = 60.967	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	IMAGE PLATE	MAR scanner 345 mm plate		2008-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	30	93.4	0.15	4	3	20419	19676	6		56.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	94.8		0.47	1.2	3.2	1938

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 1VDC	2.8	20	16736	912	96.57	0.22625	0.22581	0.23431	RANDOM	22.656

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]
1.91		3.25	-0.31		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.772
r_dihedral_angle_4_deg	20.419
r_dihedral_angle_3_deg	20.052
r_dihedral_angle_1_deg	13.505
r_scangle_it	1.448
r_angle_refined_deg	1.223
r_scbond_it	0.885
r_mcangle_it	0.732
r_mcbond_it	0.47
r_nbtor_refined	0.312
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.17
r_symmetry_vdw_refined	0.125
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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_refined
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	4786
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
SCALA	data scaling
MOLREP	phasing