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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1575)
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 3.9 68.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.068 α = 90 b = 106.07 β = 90 c = 207.674 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 2.7 35.35 99.7 0.164 0.069 0.995 10.5 6.6 53554
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 2.7 2.78 97.6 0.941 0.419 0.698 1.9 5.8 4475
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 2.7 35.35 50766 2720 99.7 0.196 0.1943 0.1968 0.2279 0.2287 RANDOM 49.103
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] 3.24 -1.41 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_3_deg 14.154 r_dihedral_angle_4_deg 13.054 r_dihedral_angle_1_deg 5.443 r_mcangle_it 1.719 r_angle_refined_deg 1.116 r_mcbond_it 1.014 r_mcbond_other 1.014 r_angle_other_deg 0.901 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_3_deg 14.154 r_dihedral_angle_4_deg 13.054 r_dihedral_angle_1_deg 5.443 r_mcangle_it 1.719 r_angle_refined_deg 1.116 r_mcbond_it 1.014 r_mcbond_other 1.014 r_angle_other_deg 0.901 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 8330 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 80
Software Software Software Name Purpose DENZO data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building