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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 5-bromopyridin-2(1H)-one (Chem 148)
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 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.433 α = 90 b = 118.814 β = 92.39 c = 65.975 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 2013-02-28 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 28.95 98.6 0.044 0.031 0.999 18 2.7 24799
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 96.3 0.374 0.282 0.864 2.2 2.2 2066
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 28.95 23499 1293 98.55 0.2138 0.2113 0.2148 0.2611 0.2603 RANDOM 56.17
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] -4.54 0.15 5.98 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_3_deg 13.983 r_dihedral_angle_4_deg 13.27 r_dihedral_angle_1_deg 5.5 r_angle_refined_deg 1.058 r_mcangle_it 0.78 r_angle_other_deg 0.719 r_mcbond_it 0.425 r_mcbond_other 0.422 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_3_deg 13.983 r_dihedral_angle_4_deg 13.27 r_dihedral_angle_1_deg 5.5 r_angle_refined_deg 1.058 r_mcangle_it 0.78 r_angle_other_deg 0.719 r_mcbond_it 0.425 r_mcbond_other 0.422 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3127 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing