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Co-crystal structure of Aquifex aeolicus Trbp111 in complex with E. coli tRNA-Ile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PYB experimental model PDB 6UFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294.15 0.2 M ammonium phosphate dibasic, 23% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.495 α = 90 b = 55.028 β = 94.42 c = 87.16 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 2022-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.64 43.09 98.79 0.0438 0.977 9.76 12.6 26578 59.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.73 0.197 0.909 0.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.64 43.09 1.33 26530 1319 98.82 0.1845 0.1825 0.184 0.2217 0.224 57.49
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.5684 f_angle_d 0.739 f_chiral_restr 0.0426 f_plane_restr 0.0048 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1628 Nucleic Acid Atoms 3262 Solvent Atoms 201 Heterogen Atoms
Software Software Software Name Purpose DIALS data scaling DIALS data reduction PHASER phasing PHENIX refinement