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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-[(4R)-6,8-dichloro-1,2,3,4-tetrahydroquinolin-4-yl]-N'-(5-fluoro-3H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1717)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 3.87 68.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.627 α = 90 b = 105.842 β = 90 c = 207.189 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ 2013-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 37.8 99.9 0.136 0.055 0.996 15.3 7 75309
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45 99.3 0.818 0.446 0.586 1.8 4.3 4363
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 4EG8 2.4 37.8 71386 3795 99.93 0.2088 0.2074 0.211 0.2364 0.2376 RANDOM 37.923
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] 2.91 -0.64 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.104 r_dihedral_angle_3_deg 13.434 r_dihedral_angle_4_deg 13.31 r_dihedral_angle_1_deg 5.397 r_angle_refined_deg 1.115 r_mcangle_it 0.975 r_angle_other_deg 0.913 r_mcbond_it 0.561 r_mcbond_other 0.561 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.104 r_dihedral_angle_3_deg 13.434 r_dihedral_angle_4_deg 13.31 r_dihedral_angle_1_deg 5.397 r_angle_refined_deg 1.115 r_mcangle_it 0.975 r_angle_other_deg 0.913 r_mcbond_it 0.561 r_mcbond_other 0.561 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8322 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 58
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building