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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[5-chloro-2-hydroxy-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1472)
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 3.91 68.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.712 α = 90 b = 106.08 β = 90 c = 206.275 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 2011-06-19 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 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 2.3 50 96.3 0.106 0.106 5.8 6.4 82816 -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 2.3 2.34 88.7 0.728 0.728 2 5.9
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 2.3 30 82518 4125 95.94 0.2043 0.2026 0.2074 0.2378 0.2402 RANDOM 47.5478
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] 7.4 -4.31 -3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.408 r_dihedral_angle_3_deg 13.902 r_dihedral_angle_4_deg 12.864 r_dihedral_angle_1_deg 5.445 r_mcangle_it 1.552 r_angle_refined_deg 1.165 r_mcbond_it 0.916 r_mcbond_other 0.916 r_angle_other_deg 0.734 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.408 r_dihedral_angle_3_deg 13.902 r_dihedral_angle_4_deg 12.864 r_dihedral_angle_1_deg 5.445 r_mcangle_it 1.552 r_angle_refined_deg 1.165 r_mcbond_it 0.916 r_mcbond_other 0.916 r_angle_other_deg 0.734 r_chiral_restr 0.065 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 8416 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 146
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection