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Crystal structure of a glutamyl-tRNA synthetase GluRS from Borrelia burgdorferi bound to glutamic acid and zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J09 PDB entry 1j09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 BobuA.01348.a.A1 at 28 mg/mL with 20 mM glutamic acid against Wiz3 screen condition A8, 20% PEG 3350, 0.2 M KNO3 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 233969a8, unique puck ID qax1-1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.83 56.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.46 α = 90 b = 110.31 β = 90 c = 197.88 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 CCD RIGAKU SATURN 944+ 2012-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.6 50 97 0.107 10.18 5.3 42317 41054 -3 39.822
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 2.6 2.67 88.9 0.374 3.39
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1j09 2.6 48.175 1.34 41004 2072 96.92 0.2264 0.2233 0.2252 0.2851 0.2853 37.4745
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 13.435 f_angle_d 0.682 f_chiral_restr 0.047 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7526 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 23
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction