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Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00071494)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOI PDB ENTRY 2WOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 15MG/ML PROTEIN IN 25MM HEPES PH 7.5 AND 50MM NABR EQUILIBRATED AGAINST 24% MPD, 10% PEG3350 AND 40MM IMIDAZOLE PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.65 α = 90 b = 63.21 β = 97.82 c = 170.5 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 CCD ADSC CCD MIRRORS 2008-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 46.8 96.7 0.14 9.4 4.3 74819 2 31.033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 91.4 0.43 3.15 4.5
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 (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 PDB ENTRY 2WOI 2.5 46.773 74819 3741 100 0.167 0.163 0.1616 0.2361 0.2342 RANDOM 22.873
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] 0.778 0.242 0.578 -1.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_4_deg 19.096 r_dihedral_angle_3_deg 17.65 r_dihedral_angle_1_deg 6.511 r_scangle_it 3.848 r_scbond_it 2.371 r_angle_refined_deg 1.682 r_mcangle_it 1.445 r_mcbond_it 0.762 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_4_deg 19.096 r_dihedral_angle_3_deg 17.65 r_dihedral_angle_1_deg 6.511 r_scangle_it 3.848 r_scbond_it 2.371 r_angle_refined_deg 1.682 r_mcangle_it 1.445 r_mcbond_it 0.762 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14837 Nucleic Acid Atoms Solvent Atoms 915 Heterogen Atoms 317
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing