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Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Tris, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.854 α = 90 b = 63.854 β = 90 c = 330.334 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 4r M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9798, 0.9801, 0.9819, 0.9727 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 40 99.4 0.048 11.7 4.1 27897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.4 40 26411 1403 99.3 0.24707 0.24491 0.28889 RANDOM 32.966
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.3 r_angle_refined_deg 1.124 r_scangle_it 0.742 r_scbond_it 0.521 r_mcangle_it 0.477 r_mcbond_it 0.253 r_nbd_refined 0.176 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.3 r_angle_refined_deg 1.124 r_scangle_it 0.742 r_scbond_it 0.521 r_mcangle_it 0.477 r_mcbond_it 0.253 r_nbd_refined 0.176 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.071 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2698 Nucleic Acid Atoms 1472 Solvent Atoms 57 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SHARP phasing