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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(quinolin-3-yl)acetamide (Chem 1691)
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 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.007 α = 90 b = 118.433 β = 91.2 c = 93.809 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 2013-03-20 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 2.3 36.15 99.8 0.101 0.061 0.998 12.6 3.7 43573
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 2.3 2.38 98.6 0.822 0.533 0.685 1.9 3.3 4228
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 2.3 36.15 41316 2227 99.68 0.2186 0.2172 0.2198 0.2446 0.2459 RANDOM 44.685
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] -0.84 0.1 4.46 -3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.657 r_dihedral_angle_4_deg 14.995 r_dihedral_angle_3_deg 14.007 r_dihedral_angle_1_deg 5.251 r_mcangle_it 1.083 r_angle_refined_deg 1.079 r_angle_other_deg 0.77 r_mcbond_it 0.616 r_mcbond_other 0.615 r_chiral_restr 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.657 r_dihedral_angle_4_deg 14.995 r_dihedral_angle_3_deg 14.007 r_dihedral_angle_1_deg 5.251 r_mcangle_it 1.083 r_angle_refined_deg 1.079 r_angle_other_deg 0.77 r_mcbond_it 0.616 r_mcbond_other 0.615 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6260 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 127
Software Software Software Name Purpose DENZO data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing