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Trypanosoma brucei PTR1 in complex with cofactor and inhibitor NMT-H024 (compound 2)
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 298 Protein solution: 6 g/L in 20 mM Tris-HCl pH 7.5, 10 mM DTT; Crystallization buffer: 0.1 M sodium citrate pH 5, 2.25 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.88 α = 90 b = 90.84 β = 115.7 c = 82.9 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 2015-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9184 Diamond I03
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 1.38 57.7 99.7 0.059 9.6 3.1 204222 2
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 1.38 1.45 99.4 0.339 2.8 3
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 2x9g 1.38 57.7 193908 10084 99.63 0.1168 0.115 0.1292 0.15046 0.1582 RANDOM 15.672
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 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.924 r_sphericity_free 32.332 r_dihedral_angle_4_deg 18.261 r_sphericity_bonded 11.965 r_dihedral_angle_3_deg 11.898 r_rigid_bond_restr 7.249 r_dihedral_angle_1_deg 7.019 r_long_range_B_refined 3.851 r_long_range_B_other 3.851 r_scangle_other 3.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.924 r_sphericity_free 32.332 r_dihedral_angle_4_deg 18.261 r_sphericity_bonded 11.965 r_dihedral_angle_3_deg 11.898 r_rigid_bond_restr 7.249 r_dihedral_angle_1_deg 7.019 r_long_range_B_refined 3.851 r_long_range_B_other 3.851 r_scangle_other 3.445 r_scbond_it 2.975 r_scbond_other 2.975 r_mcangle_it 2.542 r_mcangle_other 2.542 r_angle_refined_deg 2.391 r_mcbond_it 2.38 r_mcbond_other 2.38 r_angle_other_deg 1.192 r_chiral_restr 0.167 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7212 Nucleic Acid Atoms Solvent Atoms 905 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing