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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea (Chem 1387)
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 3.92 68.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.236 α = 90 b = 105.995 β = 90 c = 206.166 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 ADSC QUANTUM 315r 2010-11-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 ALS 8.2.2
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 2.314 50 98.1 0.11 0.11 7.9 6.7 82839 -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 2.314 2.34 93.4 0.791 0.791 2.105 6.6
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 2.314 30 82510 4106 97.03 0.1943 0.193 0.1858 0.2186 0.2101 RANDOM 37.1222
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] 1.71 -0.55 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_4_deg 14.407 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 5.5 r_mcangle_it 1.338 r_angle_refined_deg 1.177 r_mcbond_it 0.773 r_mcbond_other 0.773 r_angle_other_deg 0.729 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_4_deg 14.407 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 5.5 r_mcangle_it 1.338 r_angle_refined_deg 1.177 r_mcbond_it 0.773 r_mcbond_other 0.773 r_angle_other_deg 0.729 r_chiral_restr 0.067 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 8481 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 93
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection