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Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00065414)
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 2.5 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.94 α = 90 b = 63.3 β = 98.09 c = 169.41 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 2007-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.8 46.7 80.5 0.13 10.8 2.5 44043 2 22.916
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 2.8 2.87 79.9 0.33 4.37 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WOI 2.8 46.711 44041 2203 100 0.167 0.1642 0.2193 0.197 RANDOM 16.067
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] 1.251 0.641 -0.2 -0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.986 r_dihedral_angle_4_deg 19.79 r_dihedral_angle_3_deg 19.159 r_dihedral_angle_1_deg 7.301 r_scangle_it 3.149 r_scbond_it 1.911 r_angle_refined_deg 1.795 r_mcangle_it 1.217 r_mcbond_it 0.639 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.986 r_dihedral_angle_4_deg 19.79 r_dihedral_angle_3_deg 19.159 r_dihedral_angle_1_deg 7.301 r_scangle_it 3.149 r_scbond_it 1.911 r_angle_refined_deg 1.795 r_mcangle_it 1.217 r_mcbond_it 0.639 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.271 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_metal_ion_refined 0.014 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_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 14782 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 350
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing