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Trypanosoma brucei PTR1 in complex with inhibitor 4g (F133)
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 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.96 α = 90 b = 91.12 β = 115.9 c = 82.97 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 0.91730 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 1.74 67.43 99.6 0.064 0.074 0.037 0.998 15.3 3.9 102374 2 10.4
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 1.74 1.83 98.8 0.275 0.324 0.169 0.889 6.2 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 1.74 67.43 97271 5070 99.56 0.15599 0.15419 0.1546 0.18998 0.1901 RANDOM 16.304
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.094 r_dihedral_angle_4_deg 17.12 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 6.196 r_long_range_B_refined 5.075 r_mcangle_it 2.301 r_scbond_it 2.067 r_angle_refined_deg 1.728 r_mcbond_it 1.447 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.094 r_dihedral_angle_4_deg 17.12 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 6.196 r_long_range_B_refined 5.075 r_mcangle_it 2.301 r_scbond_it 2.067 r_angle_refined_deg 1.728 r_mcbond_it 1.447 r_chiral_restr 0.103 r_bond_refined_d 0.014 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 7305 Nucleic Acid Atoms Solvent Atoms 888 Heterogen Atoms 278
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing