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Crystal structure of rat thioredoxin, F54L mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 3 M NaCl and 0.1 M citric acid (pH 3.5)
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.21 α = 90 b = 33.35 β = 107.74 c = 67.09 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 1.752 50 99.8 0.040999999999999995 0.047 0.9990000000000001 21.95 4.06 20302
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 1.86 1.99 0.369 0.426 0.904
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KD0 1.752 44.965 20302 1016 99.852 0.192 0.1897 0.1992 0.229 0.2366 RANDOM 28.669
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] 0.62 0.762 -1.257 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.977 r_dihedral_angle_3_deg 15.532 r_lrange_it 8.058 r_lrange_other 8.014 r_scangle_it 6.58 r_scangle_other 6.577 r_dihedral_angle_1_deg 6.488 r_scbond_it 4.361 r_scbond_other 4.358 r_mcangle_other 3.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.977 r_dihedral_angle_3_deg 15.532 r_lrange_it 8.058 r_lrange_other 8.014 r_scangle_it 6.58 r_scangle_other 6.577 r_dihedral_angle_1_deg 6.488 r_scbond_it 4.361 r_scbond_other 4.358 r_mcangle_other 3.721 r_mcangle_it 3.712 r_mcbond_it 2.703 r_mcbond_other 2.701 r_angle_refined_deg 1.458 r_angle_other_deg 0.483 r_symmetry_nbd_refined 0.279 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.201 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.185 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1622 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing