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Trypanothione reductase from Trypanosoma brucei in complex with N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide
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, SITTING DROP 293.15 TbTR (10 mg/ml) in 20 mM HEPES pH 7.4; cocrystallisation with 2 mM A1/7 (incubation O/N, 283.15 K). Hanging drop vapor diffusion method + seeding, Crystallisation conditions: 100 mM Hepes pH 7-8 + 2.2-2.3 M Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.096 α = 90 b = 133.334 β = 90 c = 158.912 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 2019-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.030000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.153 158.912 99.7 0.1439 0.1499 0.04142 0.998 12.14 12.9 76940 41.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.153 2.23 98.92 1.595 0.4854 0.635 1.64 11.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WBA 2.153 102.143 76635 3832 99.71 0.242 0.2399 0.2435 0.2777 0.2798 51.112
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] -0.472 0.552 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.977 r_dihedral_angle_3_deg 14.816 r_dihedral_angle_4_deg 14.707 r_lrange_it 10.334 r_lrange_other 10.319 r_dihedral_angle_1_deg 7.203 r_scangle_it 7.014 r_scangle_other 6.991 r_mcangle_it 6.607 r_mcangle_other 6.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.977 r_dihedral_angle_3_deg 14.816 r_dihedral_angle_4_deg 14.707 r_lrange_it 10.334 r_lrange_other 10.319 r_dihedral_angle_1_deg 7.203 r_scangle_it 7.014 r_scangle_other 6.991 r_mcangle_it 6.607 r_mcangle_other 6.607 r_scbond_it 4.696 r_scbond_other 4.666 r_mcbond_it 4.618 r_mcbond_other 4.617 r_angle_refined_deg 1.522 r_angle_other_deg 1.227 r_symmetry_xyhbond_nbd_refined 0.36 r_nbd_other 0.338 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.213 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.109 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7438 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing