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Crystal structure of a glutamate tRNA ligase from Elizabethkingia meningosepticum CCUG26117 in complex with its amino acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GRI 4GRI, 2JA2, and 2WMX experimental model PDB 2JA2 4GRI, 2JA2, and 2WMX experimental model PDB 2WMX 4GRI, 2JA2, and 2WMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 MCSG1 E10 (295949e10): 200mM Ammonium tartarate dibasic, 20% (w/v) PEG3350: ElmeA.01348.a.B1.PW38364 16.23 mg/mL, direct cryo: xxk4-10
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.26 α = 90 b = 111.89 β = 90 c = 130.17 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 RAYONIX MX-300 2017-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 35.854 99.8 0.063 0.069 0.999 17.75 6.092 43563 31.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.572 0.624 0.884 3.21 6.175
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4GRI, 2JA2, and 2WMX 2 35.854 1.35 43551 1997 99.8 0.1705 0.1683 0.1717 0.2139 0.2153 37.4443
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3947 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 22
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building