☰ Navigation Tabs
Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 1-(3,4-dichlorobenzyl)-4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)(4-fluorophenyl)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 293 13-15% PEG3350, 22-24% MPD, 40 mM imidazole pH 7.5, 50 mM NaBr
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.703 α = 90 b = 63.742 β = 97.75 c = 170.096 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 2022-03-31 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 2.15 168.54 99.7 0.996 10.37 6 117489
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 2.15 2.28 0.741 2.25
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 2.15 168.54 111276 5804 99.62 0.1813 0.17902 0.1859 0.22408 0.2277 RANDOM 42.179
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] 1.52 0.87 -0.72 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_3_deg 16.135 r_long_range_B_other 8.598 r_long_range_B_refined 8.592 r_dihedral_angle_1_deg 7.019 r_scangle_other 6.011 r_mcangle_other 4.412 r_mcangle_it 4.411 r_scbond_it 3.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_3_deg 16.135 r_long_range_B_other 8.598 r_long_range_B_refined 8.592 r_dihedral_angle_1_deg 7.019 r_scangle_other 6.011 r_mcangle_other 4.412 r_mcangle_it 4.411 r_scbond_it 3.893 r_scbond_other 3.892 r_mcbond_it 3.068 r_mcbond_other 3.065 r_angle_refined_deg 1.54 r_angle_other_deg 1.27 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 14846 Nucleic Acid Atoms Solvent Atoms 595 Heterogen Atoms 453
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing