☰ Navigation Tabs
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea (Chem 1356)
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 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.058 α = 90 b = 105.956 β = 90 c = 206.672 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 2011-05-17 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 2.55 50 98.6 0.139 0.139 5.4 4.1 62918 -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 2.55 2.59 99.5 0.695 0.695 2.156 4.2
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 RIGID BODY REFINEMENT OF ISOMORPHOUS STRUCTURE THROUGHOUT PDB ENTRY 4EG8 2.55 30 62638 3189 98.01 0.2013 0.199 0.1874 0.2439 0.2234 RANDOM 37.2497
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] 3.72 -1.62 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_1_deg 5.426 r_mcangle_it 1.976 r_mcbond_it 1.088 r_mcbond_other 1.088 r_angle_refined_deg 1.081 r_angle_other_deg 0.706 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_1_deg 5.426 r_mcangle_it 1.976 r_mcbond_it 1.088 r_mcbond_other 1.088 r_angle_refined_deg 1.081 r_angle_other_deg 0.706 r_chiral_restr 0.059 r_bond_refined_d 0.006 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 8512 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 106
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction