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Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 294.15 SEEDING IN 0,1 M Hepes pH 6.8; 2.1 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 3.04 59.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.073 α = 90 b = 132.622 β = 90 c = 161.052 γ = 90
Symmetry Space Group P 21 21 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 2018-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976254 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.977 102.378 99.7 0.071 0.078 0.999 13.276 5.5 94907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.977 2.012 99.9 0.786 0.871 0.788 1.1 5.4
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 2WBA 1.977 102.378 90068 4839 99.71 0.18427 0.18309 0.1887 0.20659 0.2138 RANDOM 37.555
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] 0.47 -0.51 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.824 r_dihedral_angle_4_deg 12.641 r_dihedral_angle_3_deg 11.391 r_dihedral_angle_1_deg 5.772 r_long_range_B_refined 4.294 r_long_range_B_other 4.2 r_scangle_other 2.358 r_mcangle_it 1.946 r_mcangle_other 1.946 r_scbond_it 1.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.824 r_dihedral_angle_4_deg 12.641 r_dihedral_angle_3_deg 11.391 r_dihedral_angle_1_deg 5.772 r_long_range_B_refined 4.294 r_long_range_B_other 4.2 r_scangle_other 2.358 r_mcangle_it 1.946 r_mcangle_other 1.946 r_scbond_it 1.403 r_scbond_other 1.403 r_angle_refined_deg 1.37 r_angle_other_deg 1.285 r_mcbond_it 1.178 r_mcbond_other 1.176 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.004 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 7440 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 368
Software Software Software Name Purpose autoPROC data collection XDS data reduction Aimless data scaling pointless data scaling STARANISO data scaling Coot model building MOLREP phasing REFMAC refinement