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Crystal structure of Trypanosoma brucei trypanothione reductase (TbTR) bound to PROTAC-1
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 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.7 α = 90 b = 63.82 β = 98.1 c = 169.91 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 1.0000 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 2.09 168.22 100 0.997 9.4 5.3 124478
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 2.09 2.23 0.977
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 2.09 168.22 118269 6209 97 0.19979 0.19742 0.2041 0.24314 0.2444 RANDOM 34.578
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] 0.25 1.09 0.66 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.143 r_dihedral_angle_4_deg 18.616 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_1_deg 7.146 r_long_range_B_refined 6.212 r_long_range_B_other 6.211 r_scangle_other 5.019 r_mcangle_it 3.731 r_mcangle_other 3.731 r_scbond_it 3.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.143 r_dihedral_angle_4_deg 18.616 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_1_deg 7.146 r_long_range_B_refined 6.212 r_long_range_B_other 6.211 r_scangle_other 5.019 r_mcangle_it 3.731 r_mcangle_other 3.731 r_scbond_it 3.211 r_scbond_other 3.211 r_mcbond_it 2.597 r_mcbond_other 2.585 r_angle_refined_deg 1.515 r_angle_other_deg 1.262 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 14861 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 416
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XSCALE data scaling MOLREP phasing