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Crystal structure of Trypanosoma brucei trypanothione reductase (TbTR) bound to PROTAC-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 13-15% PEG3350, 22-24% MPD, 40 mM imidazole pH 8.0, 50 mM NaBr
Crystal Properties Matthews coefficient Solvent content 2.52 51.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.321 α = 90 b = 63.607 β = 98.23 c = 169.271 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 EIGER X 16M 2022-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.99187 ESRF ID23-1
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 2.08 46.3 97.7 0.996 8.71 6.2 126570
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 2.08 2.2 0.821 1.89
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 2.08 46.29 120263 6307 98.04 0.18067 0.17831 0.1892 0.224 0.2293 RANDOM 34.731
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] 0.02 2.14 0.44 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.698 r_dihedral_angle_4_deg 19.76 r_dihedral_angle_3_deg 15.926 r_dihedral_angle_1_deg 7.378 r_long_range_B_refined 6.471 r_long_range_B_other 6.471 r_scangle_other 5.238 r_mcangle_it 3.555 r_mcangle_other 3.555 r_scbond_it 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.698 r_dihedral_angle_4_deg 19.76 r_dihedral_angle_3_deg 15.926 r_dihedral_angle_1_deg 7.378 r_long_range_B_refined 6.471 r_long_range_B_other 6.471 r_scangle_other 5.238 r_mcangle_it 3.555 r_mcangle_other 3.555 r_scbond_it 3.47 r_scbond_other 3.47 r_mcbond_it 2.612 r_mcbond_other 2.611 r_angle_refined_deg 1.566 r_angle_other_deg 1.318 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 14857 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 512
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XSCALE data scaling MOLREP phasing