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Crystal structure of the ligase domain of fungal tRNA ligase Trl1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 ammonium sulfate, sodium chloride, HEPES
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.729 α = 90 b = 56.58 β = 90 c = 173.879 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 37.74 99.3 0.063 0.073 0.036 0.998 10.3 4.1 39302
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.1 1.029 1.184 0.575 0.793 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 37.74 37320 1924 98.99 0.1717 0.1695 0.1804 0.2144 0.2221 RANDOM 47.465
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] 3.02 0.76 -3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.985 r_dihedral_angle_4_deg 16.595 r_dihedral_angle_3_deg 14.167 r_dihedral_angle_1_deg 7.021 r_angle_refined_deg 1.386 r_angle_other_deg 1.267 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.985 r_dihedral_angle_4_deg 16.595 r_dihedral_angle_3_deg 14.167 r_dihedral_angle_1_deg 7.021 r_angle_refined_deg 1.386 r_angle_other_deg 1.267 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3113 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 68
Software Software Software Name Purpose Blu-Ice data collection MOSFLM data reduction Aimless data scaling CRANK2 phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction