3F3R

Crystal structure of yeast Thioredoxin1-glutathione mixed disulfide complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.42982.2M Ammonium Sulfate, 0.1M Sodium Acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.53α = 72.91
b = 38.81β = 87.51
c = 41.7γ = 60.58
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2008-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.833.3192.730.03331.93.917174171741113.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.989.30.05722.53.82416

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FA41.8301539615396177492.740.187160.187160.183330.2199RANDOM4.19
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]
-0.120.250.23-0.22-0.370.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.461
r_dihedral_angle_3_deg17.158
r_dihedral_angle_1_deg5.32
r_scangle_it3.076
r_scbond_it1.896
r_angle_refined_deg1.63
r_mcangle_it0.859
r_mcbond_it0.567
r_symmetry_vdw_refined0.379
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.461
r_dihedral_angle_3_deg17.158
r_dihedral_angle_1_deg5.32
r_scangle_it3.076
r_scbond_it1.896
r_angle_refined_deg1.63
r_mcangle_it0.859
r_mcbond_it0.567
r_symmetry_vdw_refined0.379
r_nbtor_refined0.306
r_symmetry_hbond_refined0.244
r_nbd_refined0.223
r_xyhbond_nbd_refined0.143
r_chiral_restr0.114
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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_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 Atoms1611
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms55

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling