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Trypanosoma brucei PTR1 in complex with cycloguanil
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 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5
Crystal Properties Matthews coefficient Solvent content 2.09 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.788 α = 90 b = 90.159 β = 115.77 c = 83.02 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 PILATUS3 6M 2017-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96863 ESRF ID30B
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 1.5 74.76 96.2 0.059 0.072 0.039 0.997 7.8 3.1 152088 2 13.6
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 1.5 1.58 94.9 0.453 0.553 0.312 0.864 2 2.9
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 1.5 66.51 144342 7608 95.94 0.17644 0.17478 0.1749 0.20745 0.2077 RANDOM 19.309
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.554 r_dihedral_angle_4_deg 19.551 r_dihedral_angle_3_deg 13.081 r_dihedral_angle_1_deg 6.173 r_long_range_B_refined 5.296 r_mcangle_it 2.682 r_scbond_it 2.52 r_angle_refined_deg 2.004 r_mcbond_it 1.853 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.554 r_dihedral_angle_4_deg 19.551 r_dihedral_angle_3_deg 13.081 r_dihedral_angle_1_deg 6.173 r_long_range_B_refined 5.296 r_mcangle_it 2.682 r_scbond_it 2.52 r_angle_refined_deg 2.004 r_mcbond_it 1.853 r_chiral_restr 0.119 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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 7277 Nucleic Acid Atoms Solvent Atoms 815 Heterogen Atoms 297
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing