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Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 294 2-2.5M sodium acetate, 0.1M sodium citrate, pH 5
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.677 α = 90 b = 90.779 β = 115.65 c = 82.81 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 2016-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.3 45.39 96.2 0.069 0.094 0.053 0.989 8.3 3 234209 11.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 94.1 0.447 0.64 0.37 0.803 2.4 2.8
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 5JDC 1.3 41.83 222393 11767 96.03 0.1277 0.126 0.1267 0.1594 0.1593 RANDOM 17.12
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] -0.03 -0.02 -0.07 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.042 r_dihedral_angle_4_deg 18.427 r_dihedral_angle_3_deg 12.029 r_rigid_bond_restr 6.793 r_dihedral_angle_1_deg 6.242 r_angle_refined_deg 1.842 r_angle_other_deg 1.663 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.042 r_dihedral_angle_4_deg 18.427 r_dihedral_angle_3_deg 12.029 r_rigid_bond_restr 6.793 r_dihedral_angle_1_deg 6.242 r_angle_refined_deg 1.842 r_angle_other_deg 1.663 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7230 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling MOLREP phasing