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IleRS in complex with a tRNA site inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ILE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.52 65.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.649 α = 90 b = 64.758 β = 107.78 c = 142.229 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 EIGER X 16M 2019-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.89 50 99.9 0.095 0.113 0.061 8.9 3.3 117006
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 0.594 0.712 0.387 0.681 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1ILE 1.895 41.58 111171 5835 99.39 0.1775 0.1766 0.1848 0.1943 0.2005 RANDOM 20.217
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] 0.48 -1.07 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.62 r_dihedral_angle_4_deg 16.664 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 6.125 r_angle_other_deg 1.261 r_angle_refined_deg 1.235 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.62 r_dihedral_angle_4_deg 16.664 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 6.125 r_angle_other_deg 1.261 r_angle_refined_deg 1.235 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7448 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing