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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea (Chem 1415)
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 68.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.449 α = 90 b = 105.728 β = 90 c = 206.592 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 2.347 50 100 0.132 0.132 6.9 7.4 80839 -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 2.347 2.39 99.9 0.876 0.876 2.077 7.2
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 2.347 30 80530 4039 99.58 0.1901 0.1886 0.1791 0.2174 0.2052 RANDOM 36.8481
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] 3.45 -1.55 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.449 r_dihedral_angle_4_deg 14.772 r_dihedral_angle_3_deg 13.743 r_dihedral_angle_1_deg 5.629 r_mcangle_it 1.753 r_angle_refined_deg 1.195 r_mcbond_it 0.998 r_mcbond_other 0.998 r_angle_other_deg 0.728 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.449 r_dihedral_angle_4_deg 14.772 r_dihedral_angle_3_deg 13.743 r_dihedral_angle_1_deg 5.629 r_mcangle_it 1.753 r_angle_refined_deg 1.195 r_mcbond_it 0.998 r_mcbond_other 0.998 r_angle_other_deg 0.728 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8450 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 102
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection