☰ Navigation Tabs
Crystal structure of the alpha subunit of glycyl tRNA synthetase (GlyRS) from Aquifex aeolicus in complex with an analog of glycyl adenylate (Gly-SA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 Drops containing 1 microliter of alpha-AaGlyRS at 15 mg/ml yielded crystals at 18C when mixed with 1 microliter of a reservoir solution containing 30% polyethylene glycol monomethyl ether 2000 and 100 mM potassium thiocyanate. Crystals were soaked for 2 days in a solution containing a final concentration of 28 mM GSAd by mixing 1.3 microliters of the drop containing crystals, 2.5 microliters of reservoir solution and 1.5 microliters of GSAd at 100 mM
Crystal Properties Matthews coefficient Solvent content 2.72 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.829 α = 90 b = 130.01 β = 90 c = 145.52 γ = 90
Symmetry Space Group P 2 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 CCD MARMOSAIC 300 mm CCD 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9785 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.81 83.43 100 0.084 9.7 4.4 47824 47824 55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.91 100 0.584 2.2 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1J5W 2.81 80.166 1.34 47741 2409 99.92 0.2396 0.2389 0.2403 0.2521 0.2517 random selection
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 16.336 f_angle_d 1.462 f_chiral_restr 0.098 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11740 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 135
Software Software Software Name Purpose PHENIX refinement Aimless data scaling MOSFLM data reduction BALBES phasing Coot model building