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X-ray crystallographic structure of E. coli K-12 glycyl-tRNA synthetase alpha subunit (glyQ)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM Morpheus buffer system 1, 0.5-3% w/v PEG 8000 and 20 % w/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 5.98 79.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.407 α = 90 b = 232.407 β = 90 c = 123.577 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2018-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97750 CHESS A1
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 3 49.43 100 0.291 0.296 0.057 0.998 11.8 26.9 68043
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 3 3.07 100 4.183 4.26 0.803 0.513 27.9
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 5F5W 3 49.43 65933 2035 99.95 0.2199 0.2187 0.2187 0.2579 0.2579 RANDOM 89.276
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] -2.15 -2.15 4.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_3_deg 20.192 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_1_deg 6.666 r_angle_refined_deg 1.306 r_chiral_restr 0.104 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9032 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing