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Crystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyces cerevisiae (oxidized form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERU PDB ENTRY 1ERU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 30% PEG 4000, 0.2M Lithium sulfate, 0.1M Tris-Hcl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.11 41.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.313 α = 90 b = 60.682 β = 90 c = 72.679 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU RAXIS IV 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54179
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 1.8 29.25 98.2 0.062 9.6 20479
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 1.8 1.86 96.9 0.348 2.1
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ERU 1.8 29.25 19400 1051 98.15 0.20053 0.19765 0.1982 0.25519 0.2546 RANDOM 21.188
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] 0.31 -0.35 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.135 r_dihedral_angle_4_deg 24.929 r_dihedral_angle_3_deg 13.174 r_dihedral_angle_1_deg 4.876 r_scangle_it 4.017 r_scbond_it 2.591 r_mcangle_it 1.45 r_angle_refined_deg 1.399 r_mcbond_it 0.907 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.135 r_dihedral_angle_4_deg 24.929 r_dihedral_angle_3_deg 13.174 r_dihedral_angle_1_deg 4.876 r_scangle_it 4.017 r_scbond_it 2.591 r_mcangle_it 1.45 r_angle_refined_deg 1.399 r_mcbond_it 0.907 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_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 1644 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing