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Crystal structure of a tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae bound to tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 NegoA.00743.a.B1.PS37949 at 19.2 mg/mL with 2 mM MgCl2, 2 mM tryptophan against morpheus screen condition C5 10% PEG 20000, 20% PEG 550 MME, 0.1 M MOPS/Hepes pH 7.5, 0.03M sodium nitrate, disodium hydrogen phosphate, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.19 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.94 α = 90 b = 59.94 β = 90 c = 162.93 γ = 120
Symmetry Space Group P 32 2 1
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 2016-08-23 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) 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 2.5 50 99.5 0.051 1 28.73 7.2 12305 -3 48.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.57 100 0.534 0.889 3.69
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 FREE R-VALUE 3TZL 2.5 43.777 1.35 12301 1315 99.54 0.1901 0.1815 0.189 0.2634 0.2664 55.8903
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 13.673 f_angle_d 0.811 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2465 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 20
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing