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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(quinolin-3-yl)propanamide (Chem 1698)
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 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.455 α = 90 b = 119.677 β = 94.17 c = 66.75 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 PIXEL DECTRIS PILATUS 6M 2014-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.95 SSRL BL12-2
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 2.75 37.81 96.2 0.054 0.03 0.999 17 4.1 13023
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 2.75 2.9 97.6 0.729 0.402 0.732 2 4.2 1938
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 2.75 37.81 12361 657 95.92 0.1834 0.1807 0.1834 0.2371 0.2376 RANDOM 78.757
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] 4.24 -2.29 -0.53 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.595 r_dihedral_angle_4_deg 18.72 r_dihedral_angle_3_deg 14.379 r_dihedral_angle_1_deg 5.527 r_mcangle_it 2.497 r_mcbond_it 1.477 r_mcbond_other 1.477 r_angle_refined_deg 1.112 r_angle_other_deg 0.716 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.595 r_dihedral_angle_4_deg 18.72 r_dihedral_angle_3_deg 14.379 r_dihedral_angle_1_deg 5.527 r_mcangle_it 2.497 r_mcbond_it 1.477 r_mcbond_other 1.477 r_angle_refined_deg 1.112 r_angle_other_deg 0.716 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3234 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 26
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing