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Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor RD117 1-[2-(Piperazin-1-yl)ethyl]-5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 Adding 5 microL of 10 mM inhibitor in DMSO to 95 microL of protein solution (10mg/ml; 20 mM TRIS, pH8.0), then mixing 2 microL of protein solution with 2 microL of well solution (0.1 M HEPES, pH 7.5, 2.0 M (NH4)2SO4).
Crystal Properties Matthews coefficient Solvent content 3.66 66.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.664 α = 90 b = 117.664 β = 90 c = 225.163 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS3 6M collimator 2016-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.797 47.7 99.4 0.137 0.146 0.049 0.998 16.8 8.6 39719 79.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.797 2.9 95 1.609 1.728 0.618 0.423 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2WOI 2.797 47.671 1.33 39619 1917 99.43 0.1985 0.1965 0.2138 0.2363 0.2522 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.665 f_angle_d 0.985 f_chiral_restr 0.043 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7472 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 251
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data scaling PHASER phasing