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Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with reveromycin A and isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.2 M ammonium sulfate, 0.1 M BIS-Tris pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.3 62.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.811 α = 90 b = 65.042 β = 107.79 c = 142.109 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9786 SSRF 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 1.9 50 99.8 0.088 0.105 0.057 0.983 6.9 3.3 116732
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 1.97 99.8 0.448 0.537 0.293 0.881 3.2
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 1.9 47.88 110905 5818 99.62 0.19429 0.19298 0.1994 0.21949 0.2246 RANDOM 33.478
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] -0.22 -1.81 3.88 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.309 r_dihedral_angle_4_deg 14.855 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 6.127 r_long_range_B_refined 4.814 r_long_range_B_other 4.671 r_scangle_other 3.137 r_mcangle_it 2.548 r_mcangle_other 2.547 r_scbond_it 1.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.309 r_dihedral_angle_4_deg 14.855 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 6.127 r_long_range_B_refined 4.814 r_long_range_B_other 4.671 r_scangle_other 3.137 r_mcangle_it 2.548 r_mcangle_other 2.547 r_scbond_it 1.955 r_scbond_other 1.953 r_mcbond_it 1.719 r_mcbond_other 1.719 r_angle_refined_deg 1.228 r_angle_other_deg 1.2 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 7425 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing