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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2-methyl-1-benzothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1540)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EG8 PDB ENTRY 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, pH 6.0-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.89 68.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.742 α = 90 b = 105.737 β = 90 c = 206.294 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 2011-10-03 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) R Sym 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 2.649 50 99.4 0.121 0.121 7.5 3.9 56308 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.649 2.7 100 0.6 0.6 1.938 3.8
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 PDB ENTRY 4EG8 2.649 29.55 56253 2858 99.34 0.2168 0.2148 0.1965 0.2552 0.2322 RANDOM 36.8537
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] 2.43 -1.53 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_4_deg 14.225 r_dihedral_angle_1_deg 5.69 r_mcangle_it 1.485 r_angle_refined_deg 1.158 r_mcbond_it 0.837 r_mcbond_other 0.837 r_angle_other_deg 0.72 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_4_deg 14.225 r_dihedral_angle_1_deg 5.69 r_mcangle_it 1.485 r_angle_refined_deg 1.158 r_mcbond_it 0.837 r_mcbond_other 0.837 r_angle_other_deg 0.72 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8502 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 97
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection