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Trypanosoma brucei PTR1 in complex with inhibitor 2d (F186)
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 5 297 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.869 α = 90 b = 90.373 β = 115.68 c = 82.933 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-F 2017-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.52 67.48 97.8 0.045 0.062 0.031 0.998 12.1 3.9 149204 2 14.2
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 1.52 1.6 96.2 0.385 0.514 0.259 0.921 2.6 3.8
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 1.52 67.48 141587 7581 97.68 0.16752 0.16616 0.1667 0.19251 0.1931 RANDOM 20.8
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 32.497 r_dihedral_angle_4_deg 20.203 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.259 r_long_range_B_refined 5.483 r_mcangle_it 2.7 r_scbond_it 2.413 r_angle_refined_deg 1.88 r_mcbond_it 1.758 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.497 r_dihedral_angle_4_deg 20.203 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.259 r_long_range_B_refined 5.483 r_mcangle_it 2.7 r_scbond_it 2.413 r_angle_refined_deg 1.88 r_mcbond_it 1.758 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 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 7390 Nucleic Acid Atoms Solvent Atoms 856 Heterogen Atoms 304
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing