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Crystal structure of resveratrol bound human tyrosyl tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N3L PDB ENTRY 1N3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 2.1 M ammonium sulfate, 0.1 M sodium phosphate monobasic / potassium phosphate dibasic, pH 6-8, 2% acetone, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.966 α = 90 b = 162.55 β = 90 c = 35.014 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2012-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5000
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.1 40 99 0.055 0.055 28.5 4.5 25654 25438 1 1 37.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 93.2 0.271 0.271 4.1 3.2 1161
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1N3L 2.1 37.01 1 25438 23994 1286 98.63 0.17723 0.17442 0.1887 0.23071 0.24 RANDOM 37.664
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 -0.51 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.613 r_dihedral_angle_4_deg 21.6 r_dihedral_angle_3_deg 17.442 r_dihedral_angle_1_deg 6.762 r_angle_refined_deg 2.071 r_angle_other_deg 1.028 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.613 r_dihedral_angle_4_deg 21.6 r_dihedral_angle_3_deg 17.442 r_dihedral_angle_1_deg 6.762 r_angle_refined_deg 2.071 r_angle_other_deg 1.028 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.011 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2636 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing