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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(5-hydroxynaphthalen-2-yl)propanamide (Chem 1781)
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 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.432 α = 90 b = 119.34 β = 93.39 c = 66.302 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 2014-10-21 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 29.09 98 0.054 0.041 0.998 15.6 2.6 31152
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 87.7 0.461 0.368 0.74 1.9 2.1 2171
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 29.09 29548 1597 97.82 0.1874 0.1853 0.1903 0.2256 0.2327 RANDOM 38.198
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] 1.49 -1.14 -0.49 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 15.489 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_1_deg 5.415 r_angle_refined_deg 1.145 r_mcangle_it 1.136 r_angle_other_deg 0.739 r_mcbond_it 0.694 r_mcbond_other 0.694 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 15.489 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_1_deg 5.415 r_angle_refined_deg 1.145 r_mcangle_it 1.136 r_angle_other_deg 0.739 r_mcbond_it 0.694 r_mcbond_other 0.694 r_chiral_restr 0.061 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 3201 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 36
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing