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Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 1-(3,4-dichlorobenzyl)-4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)carbamoyl)-1-(3-phenylpropyl)piperazin-1-ium
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, SITTING DROP 7.5 293 13-15% PEG3350, 22-24% MPD, 40 mM imidazole pH 7.5, 50 mM NaBr
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.96 α = 90 b = 63.311 β = 98.4 c = 169.112 γ = 90
Symmetry Space Group P 1 21 1
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 2022-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.42 167.3 99.8 0.997 11.56 5.8 81239
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.57 0.764 2.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.42 55.83 77174 4052 99.8 0.19329 0.18988 0.195 0.25741 0.2574 RANDOM 40.974
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] 2.07 0.87 -1.53 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.017 r_dihedral_angle_4_deg 19.508 r_dihedral_angle_3_deg 17.713 r_dihedral_angle_1_deg 7.706 r_long_range_B_refined 7.268 r_long_range_B_other 7.268 r_scangle_other 5.356 r_mcangle_it 4.627 r_mcangle_other 4.627 r_scbond_it 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.017 r_dihedral_angle_4_deg 19.508 r_dihedral_angle_3_deg 17.713 r_dihedral_angle_1_deg 7.706 r_long_range_B_refined 7.268 r_long_range_B_other 7.268 r_scangle_other 5.356 r_mcangle_it 4.627 r_mcangle_other 4.627 r_scbond_it 3.46 r_scbond_other 3.46 r_mcbond_it 3.117 r_mcbond_other 3.115 r_angle_refined_deg 1.57 r_angle_other_deg 1.238 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 14847 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 436
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing