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Crystal structure of arginyl-tRNA_synthetase from Neisseria gonorrhoeae in complex with arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OBY PDB entry 4OBY in 3 domains as suggested by MORDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 20 mg/mL NegoA.00164.a.B1.PS38233 against Microlytic MCSG1 G6 (0.1 M sodium acetate/hydrochloric acid, pH 4.5, 25% w/v PEG3350) + 2 mM magnesium chloride, 2 mM AMPPNP, 2 mM arginine, Tray 290716 G6, puck PRP0-2
Crystal Properties Matthews coefficient Solvent content 2.96 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.9 α = 90 b = 93.47 β = 108.07 c = 78.57 γ = 90
Symmetry Space Group P 1 21 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 2017-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.7 34.182 99.7 0.03 0.035 1 22.92 3.777 81144 -3 25.11
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 1.7 1.74 99.8 0.513 0.599 0.903 2.38 3.768
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 PDB entry 4OBY in 3 domains as suggested by MORDA 1.7 34.182 1.35 81057 2010 99.73 0.1627 0.1622 0.1635 0.1839 0.1861 0 34.6851
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 13.057 f_angle_d 0.868 f_chiral_restr 0.06 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4268 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms 18
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction