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Crystal structure of Thioredoxin reductase from Brugia Malayi
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 22% MPD, 0.1M Tris/HCl pH8, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 2.92 57.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.921 α = 90 b = 258.985 β = 90 c = 129.067 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 2.55 48.9 100 0.032 1 28.8 6.6 80241
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 2.55 2.6 100 0.82 0.8 2.3 6.8
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 2.55 48.9 76369 3847 99.92 0.1987 0.1969 0.1996 0.2375 0.2373 RANDOM 94.366
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] -2.21 -0.88 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.561 r_dihedral_angle_4_deg 17.536 r_dihedral_angle_3_deg 16.239 r_dihedral_angle_1_deg 7.802 r_angle_refined_deg 1.564 r_angle_other_deg 1.287 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.561 r_dihedral_angle_4_deg 17.536 r_dihedral_angle_3_deg 16.239 r_dihedral_angle_1_deg 7.802 r_angle_refined_deg 1.564 r_angle_other_deg 1.287 r_chiral_restr 0.072 r_bond_refined_d 0.009 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 13255 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing