3DGZ | pdb_00003dgz

Crystal Structure of Mouse Mitochondrial Thioredoxin Reductase, C-terminal 3-residue truncation

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1 M MES, 22% PEG 6000, 2% Ethylene Glycol, pH 5.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	59.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.507	α = 90
b = 110.507	β = 90
c = 208.025	γ = 90

Symmetry
Space Group	I 41 2 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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2005-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5417

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	2.25	30	95.1	0.075	23.5	5.23		29523

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)
1	2.25	2.29	95.8		0.448	6.67		1454

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	2.25	15.45	29515	2967	95.23	0.2	0.193	0.19	0.258	0.26	RANDOM	39.885

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]
-0.42			-0.42		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.385
r_dihedral_angle_4_deg	18.879
r_dihedral_angle_3_deg	17.909
r_dihedral_angle_1_deg	7.624
r_scangle_it	4.207
r_scbond_it	2.996
r_angle_refined_deg	2.185
r_mcangle_it	1.578
r_mcbond_it	1.056
r_symmetry_vdw_refined	0.339

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.385
r_dihedral_angle_4_deg	18.879
r_dihedral_angle_3_deg	17.909
r_dihedral_angle_1_deg	7.624
r_scangle_it	4.207
r_scbond_it	2.996
r_angle_refined_deg	2.185
r_mcangle_it	1.578
r_mcbond_it	1.056
r_symmetry_vdw_refined	0.339
r_nbtor_refined	0.303
r_nbd_refined	0.228
r_chiral_restr	0.176
r_xyhbond_nbd_refined	0.154
r_symmetry_hbond_refined	0.092
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3679
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	92

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.