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Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex with auranofin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TR1 3QFA_A; 4TR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294.15 14% MPD, 0.1 M Tris/HCl pH 7.5, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 3.03 59.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.333 α = 90 b = 261.659 β = 90 c = 130.289 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2020-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.1 49.31 100 0.083 0.998 18.6 12.8 46008
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 100 0.688 0.904 3.1 13.6
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 3QFA_A; 4TR1 3.1 49.36 43675 2303 99.93 0.1882 0.1861 0.1898 0.2287 0.2271 RANDOM 117.47
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] -2.58 1.9 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.892 r_dihedral_angle_4_deg 21.506 r_dihedral_angle_3_deg 17.742 r_dihedral_angle_1_deg 7.637 r_angle_refined_deg 1.569 r_angle_other_deg 1.25 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.892 r_dihedral_angle_4_deg 21.506 r_dihedral_angle_3_deg 17.742 r_dihedral_angle_1_deg 7.637 r_angle_refined_deg 1.569 r_angle_other_deg 1.25 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13184 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing