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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 6-amino-2H-chromen-2-one (Chem 744)
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 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.097 α = 90 b = 119.271 β = 92.85 c = 66.14 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 2013-05-20 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 2.05 27.82 98.2 0.055 0.037 0.998 10.6 2.8 31011
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 2.05 2.11 89.6 0.336 0.27 0.799 2.4 2 2186
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 2.05 27.82 29417 1590 98.13 0.186 0.1843 0.1899 0.2176 0.2176 RANDOM 39.798
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] 1.16 0.77 -0.42 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.86 r_dihedral_angle_4_deg 15.325 r_dihedral_angle_3_deg 13.465 r_dihedral_angle_1_deg 5.349 r_mcangle_it 1.701 r_angle_refined_deg 1.086 r_mcbond_it 0.988 r_mcbond_other 0.987 r_angle_other_deg 0.721 r_chiral_restr 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.86 r_dihedral_angle_4_deg 15.325 r_dihedral_angle_3_deg 13.465 r_dihedral_angle_1_deg 5.349 r_mcangle_it 1.701 r_angle_refined_deg 1.086 r_mcbond_it 0.988 r_mcbond_other 0.987 r_angle_other_deg 0.721 r_chiral_restr 0.056 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 3172 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing