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Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor EP127 (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 PDB ENTRY 2WOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 0.1M HEPES, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.6 65.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.2 α = 90 b = 117.2 β = 90 c = 224.6 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 100 CCD RAYONIX MX-300 2013-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 66.75 99.8 0.072 8 56511
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 100 0.53 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2WOI 2.5 66 56609 52052 2779 99.9 0.235 0.234 0.2305 0.258 0.2586 RANDOM 67.54
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 r_dihedral_angle_2_deg 34.155 r_dihedral_angle_3_deg 15.884 r_dihedral_angle_4_deg 13.396 r_dihedral_angle_1_deg 6.117 r_long_range_B_refined 5.431 r_long_range_B_other 5.429 r_mcangle_it 3.44 r_mcangle_other 3.44 r_scangle_other 3.32 r_mcbond_it 2.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.155 r_dihedral_angle_3_deg 15.884 r_dihedral_angle_4_deg 13.396 r_dihedral_angle_1_deg 6.117 r_long_range_B_refined 5.431 r_long_range_B_other 5.429 r_mcangle_it 3.44 r_mcangle_other 3.44 r_scangle_other 3.32 r_mcbond_it 2.161 r_mcbond_other 2.161 r_scbond_it 2.045 r_scbond_other 2.045 r_angle_refined_deg 0.909 r_angle_other_deg 0.657 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7368 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 236
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling