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Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 1 (NMT-C0003)
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 2.14 42.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.86 α = 90 b = 90.7 β = 115.73 c = 82.95 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 2015-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91731 Diamond I04-1
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 1.42 57.67 99.8 0.053 0.062 0.031 0.998 11 3.8 187289 2 11.1
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 1.42 1.5 99.4 0.29 0.337 0.17 0.926 2.2 3.9
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 1.42 57.67 178068 9189 99.73 0.13948 0.13764 0.138 0.1753 0.1753 RANDOM 13.928
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.505 r_sphericity_free 25.894 r_dihedral_angle_4_deg 17.009 r_dihedral_angle_3_deg 12.057 r_sphericity_bonded 11.738 r_dihedral_angle_1_deg 5.797 r_long_range_B_refined 3.256 r_scbond_it 1.931 r_rigid_bond_restr 1.856 r_mcangle_it 1.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.505 r_sphericity_free 25.894 r_dihedral_angle_4_deg 17.009 r_dihedral_angle_3_deg 12.057 r_sphericity_bonded 11.738 r_dihedral_angle_1_deg 5.797 r_long_range_B_refined 3.256 r_scbond_it 1.931 r_rigid_bond_restr 1.856 r_mcangle_it 1.777 r_angle_refined_deg 1.698 r_mcbond_it 1.428 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7259 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 301
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing