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Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase mutant (32A NTD) bound to tRNA(Pyl)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 Bis-Tris, MgCl2, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.62 α = 90 b = 72.62 β = 90 c = 238.58 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M-F 2017-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.76 49.33 99.9 25.7 9.7 19670
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 FREE R-VALUE 2.76 49.33 1.35 19633 1963 99.76 0.2107 0.2064 0.2127 0.249 0.245
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 12.347 f_angle_d 0.636 f_chiral_restr 0.034 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1368 Nucleic Acid Atoms 3020 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing