3ITJ

Crystal structure of Saccharomyces cerevisiae thioredoxin reductase 1 (Trr1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VDCPDB entry 1VDC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42932.7 M Sodium citrate pH 4.0, 12% PEG 3000, 0.1 M Trimethylamine hydrochloride. Drop volume of 6.0 ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.975α = 90
b = 135.411β = 89.95
c = 75.819γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMAR CCD 165 mmmirrors2004-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.431LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.45097.030.09917.66.1464884.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.46299.30.324.46

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1VDC2.45046488245997.030.170530.16930.19356RANDOM20.636
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]
-3.221.94-1.354.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.28
r_dihedral_angle_4_deg18.561
r_dihedral_angle_3_deg17.859
r_dihedral_angle_1_deg7.114
r_scangle_it4.326
r_scbond_it2.938
r_angle_refined_deg2.253
r_mcangle_it1.638
r_mcbond_it0.993
r_chiral_restr0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.28
r_dihedral_angle_4_deg18.561
r_dihedral_angle_3_deg17.859
r_dihedral_angle_1_deg7.114
r_scangle_it4.326
r_scbond_it2.938
r_angle_refined_deg2.253
r_mcangle_it1.638
r_mcbond_it0.993
r_chiral_restr0.141
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
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 AtomsNumber
Protein Atoms9262
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms290

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling