2HSH

Crystal structure of C73S mutant of human thioredoxin-1 oxidized with H2O2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ERTPDB entry 1ERT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.829850% MPD, 10 mM sodium acetate, 8% H2O2, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8934.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.166α = 90
b = 26.375β = 95.47
c = 51.1γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVosmic mirrors2005-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.3522.486.20.02830.13.21604618.9
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)
1.351.450.60.143.92981

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1ERT1.3522.37160461604688286.240.124880.122570.16843RANDOM10.477
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]
-0.28-0.150.41-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.134
r_dihedral_angle_3_deg13.231
r_sphericity_free10.579
r_dihedral_angle_1_deg6.01
r_scangle_it5.101
r_scbond_it3.752
r_sphericity_bonded3.552
r_mcangle_it2.345
r_rigid_bond_restr2.027
r_mcbond_it2.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.134
r_dihedral_angle_3_deg13.231
r_sphericity_free10.579
r_dihedral_angle_1_deg6.01
r_scangle_it5.101
r_scbond_it3.752
r_sphericity_bonded3.552
r_mcangle_it2.345
r_rigid_bond_restr2.027
r_mcbond_it2.003
r_angle_refined_deg1.626
r_angle_other_deg0.953
r_mcbond_other0.692
r_symmetry_vdw_refined0.621
r_symmetry_hbond_refined0.374
r_xyhbond_nbd_refined0.261
r_nbd_refined0.251
r_symmetry_vdw_other0.201
r_nbd_other0.192
r_nbtor_refined0.183
r_chiral_restr0.11
r_nbtor_other0.086
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms971
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling