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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 1-(4-BROMOPHENYL)METHANAMINE (Chem 707)
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 = 90.182 α = 90 b = 119.174 β = 91.36 c = 94.341 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 2013-04-05 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 32.98 97.6 0.078 0.068 0.997 9.1 2.1 49246
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 89.8 0.5 0.44 0.673 1.7 1.8 3909
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 29.14 46700 2535 97.46 0.2222 0.2206 0.2234 0.2521 0.2565 RANDOM 38.299
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] -0.98 -0.07 0.33 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.352 r_dihedral_angle_4_deg 14.348 r_dihedral_angle_3_deg 14.185 r_dihedral_angle_1_deg 5.531 r_angle_refined_deg 1.081 r_mcangle_it 0.838 r_angle_other_deg 0.778 r_mcbond_it 0.488 r_mcbond_other 0.488 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.352 r_dihedral_angle_4_deg 14.348 r_dihedral_angle_3_deg 14.185 r_dihedral_angle_1_deg 5.531 r_angle_refined_deg 1.081 r_mcangle_it 0.838 r_angle_other_deg 0.778 r_mcbond_it 0.488 r_mcbond_other 0.488 r_chiral_restr 0.058 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 6285 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 115
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction RESOLVE phasing