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Crystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyces cerevisiae (reduced 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 4.6 291 0.2M ammonium sulfate, 0.1M sodium acetate, 8% PEG 4000, 15% glycerol, 8mM DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.575 α = 90 b = 49.575 β = 90 c = 94.554 γ = 120
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 2005-12-31 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 2.1 25.41 93.5 0.111 14.4 14192 19.05
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) 2.1 2.21 91.9 0.393 3.6 2040
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ERU 2.1 25.41 13460 724 93.31 0.16258 0.15954 0.2202 0.1863 RANDOM 16.653
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] -0.21 -0.1 -0.21 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.122 r_dihedral_angle_3_deg 14.66 r_dihedral_angle_4_deg 14.05 r_dihedral_angle_1_deg 6.099 r_scangle_it 2.431 r_mcangle_it 1.96 r_scbond_it 1.57 r_angle_refined_deg 1.565 r_mcbond_it 1.243 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.122 r_dihedral_angle_3_deg 14.66 r_dihedral_angle_4_deg 14.05 r_dihedral_angle_1_deg 6.099 r_scangle_it 2.431 r_mcangle_it 1.96 r_scbond_it 1.57 r_angle_refined_deg 1.565 r_mcbond_it 1.243 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling MOLREP phasing