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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1433) and ATP analog AMPPCP
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 = 88.267 α = 90 b = 105.88 β = 90 c = 206.676 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 PIXEL DECTRIS PILATUS 6M 2011-12-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.253 39.967 99.8 0.177 11.2 7.8 91992 91992
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 2.253 2.38 99.9 0.012 1.244 0.6 7.8 13304
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 2.253 30 91918 4606 99.68 0.1831 0.1816 0.1883 0.2114 0.2156 RANDOM 38.6552
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] 1.06 -0.06 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 15.696 r_dihedral_angle_3_deg 13.898 r_dihedral_angle_1_deg 5.508 r_mcangle_it 1.821 r_angle_refined_deg 1.192 r_mcbond_it 1.05 r_mcbond_other 1.05 r_angle_other_deg 0.729 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 15.696 r_dihedral_angle_3_deg 13.898 r_dihedral_angle_1_deg 5.508 r_mcangle_it 1.821 r_angle_refined_deg 1.192 r_mcbond_it 1.05 r_mcbond_other 1.05 r_angle_other_deg 0.729 r_chiral_restr 0.068 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 8508 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 138
Software Software Software Name Purpose DENZO data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction