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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2,5-dichlorothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1509)
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 = 88.138 α = 90 b = 106.171 β = 90 c = 206.975 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 2.313 38.567 99.9 0.161 12.9 8.2 85493 85493
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 2.313 2.44 99.9 0.011 1.109 0.7 7.9 12305
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 2.313 30 85417 4273 99.86 0.1814 0.1805 0.1868 0.1982 0.203 RANDOM 37.7066
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] 1.64 -0.97 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.116 r_dihedral_angle_4_deg 13.961 r_dihedral_angle_3_deg 13.404 r_dihedral_angle_1_deg 5.398 r_mcangle_it 1.599 r_angle_refined_deg 1.149 r_mcbond_it 0.922 r_mcbond_other 0.922 r_angle_other_deg 0.732 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.116 r_dihedral_angle_4_deg 13.961 r_dihedral_angle_3_deg 13.404 r_dihedral_angle_1_deg 5.398 r_mcangle_it 1.599 r_angle_refined_deg 1.149 r_mcbond_it 0.922 r_mcbond_other 0.922 r_angle_other_deg 0.732 r_chiral_restr 0.066 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 8516 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 105
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction