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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-ethynylbenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1478)
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 3.93 68.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.026 α = 90 b = 105.902 β = 90 c = 207.016 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 MARMOSAIC 325 mm CCD 2011-07-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
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 2.65 50 100 0.11 0.11 7.1 4 56721 -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 2.65 2.7 100 0.692 0.692 2.045 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4EG8 2.65 30 56449 2859 99.2 0.1819 0.1802 0.2135 0.1881 RANDOM 44.8737
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] 2.29 -0.79 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 16.02 r_dihedral_angle_3_deg 14.146 r_dihedral_angle_1_deg 5.339 r_mcangle_it 1.903 r_angle_refined_deg 1.125 r_mcbond_it 1.096 r_mcbond_other 1.096 r_angle_other_deg 0.72 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 16.02 r_dihedral_angle_3_deg 14.146 r_dihedral_angle_1_deg 5.339 r_mcangle_it 1.903 r_angle_refined_deg 1.125 r_mcbond_it 1.096 r_mcbond_other 1.096 r_angle_other_deg 0.72 r_chiral_restr 0.061 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 8492 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 85
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection