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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine (Chem 1655)
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 3.89 68.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.794 α = 90 b = 106.021 β = 90 c = 207.659 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 MARMOSAIC 325 mm CCD 2014-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 2.35 39.43 100 0.174 0.046 0.999 17.5 15 80610
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 2.35 2.4 100 1.88 0.496 0.689 1.8 15.1 4543
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 2.35 38.67 76494 4035 99.97 0.2016 0.2001 0.2028 0.2285 0.2325 RANDOM 51.265
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] 7.16 -2.74 -4.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.117 r_dihedral_angle_3_deg 13.571 r_dihedral_angle_4_deg 13.19 r_dihedral_angle_1_deg 5.277 r_mcangle_it 2.038 r_mcbond_it 1.247 r_mcbond_other 1.246 r_angle_refined_deg 1.091 r_angle_other_deg 0.884 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.117 r_dihedral_angle_3_deg 13.571 r_dihedral_angle_4_deg 13.19 r_dihedral_angle_1_deg 5.277 r_mcangle_it 2.038 r_mcbond_it 1.247 r_mcbond_other 1.246 r_angle_refined_deg 1.091 r_angle_other_deg 0.884 r_chiral_restr 0.063 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 8259 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 80
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building