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Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex with NADP(H)
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 8 294.15 0.1M Tris/HCl pH 8, 5mM DTT, 20% MPD
Crystal Properties Matthews coefficient Solvent content 3.15 60.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.39 α = 90 b = 260.287 β = 90 c = 130.333 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 2020-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.999900 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 2.8 49.13 99.9 0.046 0.999 22.2 7.2 61904
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 2.8 2.87 0.564 0.874 3.1 7.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QFA_A, 4TR1 2.8 49.13 58828 3054 99.9 0.1975 0.196 0.2286 0.2258 RANDOM 103.503
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] -1.71 0.77 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.983 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 17.041 r_dihedral_angle_1_deg 7.673 r_angle_refined_deg 1.621 r_angle_other_deg 1.299 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.983 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 17.041 r_dihedral_angle_1_deg 7.673 r_angle_refined_deg 1.621 r_angle_other_deg 1.299 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13176 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing