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Crystal structure of rat thioredoxin, Wild-type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 15–16% PEG-3350, 9% glycerol, and 0.1 M citric acid (pH 3.5)
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.64 α = 90 b = 74.3 β = 101.68 c = 53.95 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 225 mm CCD 2022-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.11 50 99.5 0.09699999999999999 0.113 0.997 14.07 3.75 13638
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.24 0.672 0.787 0.755
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4OO5 2.112 43.057 13637 682 99.81 0.184 0.1818 0.1927 0.2299 0.2385 29.754
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] -0.997 -0.113 -0.344 1.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.451 r_dihedral_angle_6_deg 16.407 r_lrange_it 7.767 r_lrange_other 7.767 r_dihedral_angle_1_deg 7.04 r_scangle_it 5.97 r_scangle_other 5.967 r_mcangle_it 3.85 r_mcangle_other 3.848 r_scbond_it 3.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.451 r_dihedral_angle_6_deg 16.407 r_lrange_it 7.767 r_lrange_other 7.767 r_dihedral_angle_1_deg 7.04 r_scangle_it 5.97 r_scangle_other 5.967 r_mcangle_it 3.85 r_mcangle_other 3.848 r_scbond_it 3.847 r_scbond_other 3.845 r_mcbond_it 2.581 r_mcbond_other 2.581 r_angle_refined_deg 1.369 r_angle_other_deg 0.466 r_nbd_refined 0.232 r_nbd_other 0.226 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_refined 0.206 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.181 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1628 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing