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Trypanosoma brucei PTR1 in complex with inhibitor NMT-H037 (compound 7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution: 8 g/L in 20 mM Tris-HCl pH 7.5, 10mM DTT; Crystallization buffer: 0.1 M Sodium Citrate pH 5, 2.25 M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.33 α = 90 b = 89.37 β = 115.41 c = 82.75 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 2M 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 65.96 88.2 0.056 7.8 2 85165 2 29.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 81.2 0.36 1.8 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2X9G 1.76 65.96 80554 4279 87.68 0.17849 0.17601 0.22488 0.2214 RANDOM 22.486
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 34.93 r_dihedral_angle_4_deg 19.364 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 7.275 r_long_range_B_refined 5.283 r_mcangle_it 2.717 r_scbond_it 2.416 r_angle_refined_deg 1.938 r_mcbond_it 1.87 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.93 r_dihedral_angle_4_deg 19.364 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 7.275 r_long_range_B_refined 5.283 r_mcangle_it 2.717 r_scbond_it 2.416 r_angle_refined_deg 1.938 r_mcbond_it 1.87 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 7211 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 263
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing