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Crystal Structure of human lysyl-tRNA synthetase with acetyllysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 289 0.06 M Morpheus Divalents, 0.1 M Morpheus Buffer system 1, pH 6.5 and 30% Morpheus Precipitant Mix 2
Crystal Properties Matthews coefficient Solvent content 2.79 55.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.337 α = 90 b = 90.469 β = 90 c = 107.201 γ = 90
Symmetry Space Group P 21 21 21
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 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.97921 NFPSS BL18U
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 2.26 23.44 99.51 0.2169 0.2258 0.06223 0.994 7.77 13.4 114081 35.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.341 0.888
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 2.26 23.44 1.36 114080 3804 99.51 0.2397 0.2388 0.2389 0.2635 0.2634 54.33
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 14.4331 f_angle_d 0.5755 f_chiral_restr 0.0421 f_plane_restr 0.0063 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7944 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing