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Crystal structure of C73S mutant of human thioredoxin-1 oxidized with H2O2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT PDB entry 1ERT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.8 298 50% MPD, 10 mM sodium acetate, 8% H2O2, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.166 α = 90 b = 26.375 β = 95.47 c = 51.1 γ = 90
Symmetry Space Group C 1 2 1
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 osmic mirrors 2005-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.35 22.4 86.2 0.028 30.1 3.2 16046 18.9
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) 1.35 1.4 50.6 0.14 3.9 2 981
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1ERT 1.35 22.37 16046 16046 882 86.24 0.12488 0.12257 0.1292 0.16843 0.1701 RANDOM 10.477
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 -0.15 0.41 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_3_deg 13.231 r_sphericity_free 10.579 r_dihedral_angle_1_deg 6.01 r_scangle_it 5.101 r_scbond_it 3.752 r_sphericity_bonded 3.552 r_mcangle_it 2.345 r_rigid_bond_restr 2.027 r_mcbond_it 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_3_deg 13.231 r_sphericity_free 10.579 r_dihedral_angle_1_deg 6.01 r_scangle_it 5.101 r_scbond_it 3.752 r_sphericity_bonded 3.552 r_mcangle_it 2.345 r_rigid_bond_restr 2.027 r_mcbond_it 2.003 r_angle_refined_deg 1.626 r_angle_other_deg 0.953 r_mcbond_other 0.692 r_symmetry_vdw_refined 0.621 r_symmetry_hbond_refined 0.374 r_xyhbond_nbd_refined 0.261 r_nbd_refined 0.251 r_symmetry_vdw_other 0.201 r_nbd_other 0.192 r_nbtor_refined 0.183 r_chiral_restr 0.11 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling