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Crystal structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA aminoacylation and nuclear export cofactor Arc1p reveal a novel function for an old fold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 1.8-1.9 M (NH4)2SO4, 200 mM NaI, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.959 α = 90 b = 107.113 β = 90 c = 167.865 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 225 mm CCD 2004-12-17 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2005-04-29 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97925 ESRF ID23-1 2 SYNCHROTRON SLS BEAMLINE X06SA 0.97912, 0.97934, 0.95372 SLS X06SA
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 1.9 80 99.9 0.073 13.2 4.7 37390 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.9 2 99.9 0.36 4.2 4.5 5271
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 (All) 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 MAD THROUGHOUT none 1.9 80 -3 35521 35496 1892 99.93 0.21643 0.21643 0.21408 0.2276 0.26202 0.2759 RANDOM 24.734
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] 3.63 -1.49 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.965 r_dihedral_angle_4_deg 18.84 r_dihedral_angle_3_deg 16.23 r_dihedral_angle_1_deg 6.922 r_scangle_it 3.391 r_scbond_it 2.185 r_angle_refined_deg 1.469 r_mcangle_it 1.348 r_angle_other_deg 0.945 r_mcbond_it 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.965 r_dihedral_angle_4_deg 18.84 r_dihedral_angle_3_deg 16.23 r_dihedral_angle_1_deg 6.922 r_scangle_it 3.391 r_scbond_it 2.185 r_angle_refined_deg 1.469 r_mcangle_it 1.348 r_angle_other_deg 0.945 r_mcbond_it 0.8 r_symmetry_metal_ion_refined 0.469 r_symmetry_vdw_refined 0.383 r_symmetry_hbond_refined 0.295 r_symmetry_vdw_other 0.286 r_nbd_refined 0.233 r_mcbond_other 0.201 r_xyhbond_nbd_refined 0.2 r_nbd_other 0.197 r_nbtor_refined 0.183 r_nbtor_other 0.09 r_chiral_restr 0.087 r_metal_ion_refined 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2729 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXCD phasing SHELXD phasing SOLVE phasing RESOLVE phasing