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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 6-bromopyridin-3-amine (Chem 475)
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 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.245 α = 90 b = 119.221 β = 91.28 c = 94.232 γ = 90
Symmetry Space Group C 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 2013-01-09 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 2.2 36.37 98.8 0.104 0.072 0.996 9.3 2.9 49893
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 2.2 2.27 94.8 0.579 0.427 0.672 1.7 2.4 4115
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 2.2 30 47387 2503 98.77 0.2068 0.2051 0.2081 0.2401 0.2417 RANDOM 37.619
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] -0.44 0.52 1.09 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_4_deg 16.403 r_dihedral_angle_3_deg 14.04 r_dihedral_angle_1_deg 5.346 r_angle_refined_deg 1.124 r_mcangle_it 0.861 r_angle_other_deg 0.782 r_mcbond_it 0.488 r_mcbond_other 0.488 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_4_deg 16.403 r_dihedral_angle_3_deg 14.04 r_dihedral_angle_1_deg 5.346 r_angle_refined_deg 1.124 r_mcangle_it 0.861 r_angle_other_deg 0.782 r_mcbond_it 0.488 r_mcbond_other 0.488 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6396 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing