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Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor F194
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.332 α = 90 b = 90.498 β = 115.43 c = 83.1 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 2018-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
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 1.76 90.5 98.8 0.044 0.065 0.034 0.998 12.9 3.6 97143 26.3
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 1.76 1.86 0.6 0.816 0.414 0.72 2 3.7
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 1.76 66.17 92122 4991 98.7 0.19603 0.19359 0.197 0.23931 0.2419 RANDOM 32.862
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] -0.99 -1.23 3.58 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.788 r_dihedral_angle_4_deg 17.994 r_dihedral_angle_3_deg 14.346 r_dihedral_angle_1_deg 6.524 r_long_range_B_refined 6.113 r_mcangle_it 3.822 r_scbond_it 3.237 r_mcbond_it 2.84 r_angle_refined_deg 1.557 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.788 r_dihedral_angle_4_deg 17.994 r_dihedral_angle_3_deg 14.346 r_dihedral_angle_1_deg 6.524 r_long_range_B_refined 6.113 r_mcangle_it 3.822 r_scbond_it 3.237 r_mcbond_it 2.84 r_angle_refined_deg 1.557 r_chiral_restr 0.101 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 7295 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing