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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitorN-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1708)
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 3.91 68.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.516 α = 90 b = 106.128 β = 90 c = 207.106 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 PIXEL DECTRIS PILATUS 6M 2014-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.954 SSRL BL12-2
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 2.3 38.59 99.9 0.098 0.041 0.999 17 6.8 86315
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 2.3 2.34 100 0.995 0.406 0.742 2.2 6.9 4500
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 4EG8 2.3 38.59 81926 4315 99.83 0.2016 0.2004 0.2251 0.202 RANDOM 44.603
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] 3.83 -1.74 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.497 r_dihedral_angle_4_deg 14.928 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 5.261 r_mcangle_it 1.911 r_mcbond_it 1.13 r_mcbond_other 1.13 r_angle_refined_deg 1.105 r_angle_other_deg 0.881 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.497 r_dihedral_angle_4_deg 14.928 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 5.261 r_mcangle_it 1.911 r_mcbond_it 1.13 r_mcbond_other 1.13 r_angle_refined_deg 1.105 r_angle_other_deg 0.881 r_chiral_restr 0.062 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 8226 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 57
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building