☰ Navigation Tabs
Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with tRNA(Ile) and isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D5C experimental model PDB 1FFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH5.5, 25% PEG3350, 0.06 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.428 α = 90 b = 173.521 β = 91.16 c = 171.803 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.9785 NFPSS BL19U1
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 2.8 48.73 98.3 0.077 0.091 0.049 0.997 12.1 3.3 75496
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 2.8 2.86 99.1 0.607 0.718 0.379 0.771 3.5
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 MOLECULAR REPLACEMENT THROUGHOUT 2.8 48.73 71849 3604 98.18 0.23171 0.22991 0.234 0.26793 0.2698 RANDOM 60.812
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] 3.92 -3.05 -1.06 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_dihedral_angle_3_deg 18.061 r_dihedral_angle_4_deg 16.191 r_long_range_B_refined 6.288 r_long_range_B_other 6.284 r_dihedral_angle_1_deg 5.573 r_mcangle_it 4.329 r_mcangle_other 4.329 r_scangle_other 4.284 r_scbond_it 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_dihedral_angle_3_deg 18.061 r_dihedral_angle_4_deg 16.191 r_long_range_B_refined 6.288 r_long_range_B_other 6.284 r_dihedral_angle_1_deg 5.573 r_mcangle_it 4.329 r_mcangle_other 4.329 r_scangle_other 4.284 r_scbond_it 2.701 r_mcbond_it 2.7 r_mcbond_other 2.7 r_scbond_other 2.68 r_angle_other_deg 1.295 r_angle_refined_deg 1.187 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15068 Nucleic Acid Atoms 3102 Solvent Atoms 208 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing