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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 2-aminoquinolin-8-ol (Chem 89)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.244 α = 90 b = 119.366 β = 93.61 c = 65.66 γ = 90
Symmetry Space Group I 1 2 1
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 RIGAKU SATURN 944 2013-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.1 37.27 95.5 0.062 0.048 0.997 9.8 2.4 27892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 69.5 0.544 0.43 0.722 1.7 2 1663
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 3LC0 2.1 37.27 26457 1435 95.35 0.1858 0.1841 0.1889 0.2191 0.2224 RANDOM 52.992
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] 1.17 -1.12 -0.82 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 15.586 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_1_deg 5.823 r_mcangle_it 1.757 r_angle_refined_deg 1.152 r_mcbond_it 1.06 r_mcbond_other 1.059 r_angle_other_deg 0.723 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 15.586 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_1_deg 5.823 r_mcangle_it 1.757 r_angle_refined_deg 1.152 r_mcbond_it 1.06 r_mcbond_other 1.059 r_angle_other_deg 0.723 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3285 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 61
Software Software Software Name Purpose DENZO data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing