☰ Navigation Tabs
Crystal structure of Glutamine-tRNA ligase /Glutaminyl-tRNA synthetase (GlnRS) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NYL PDB entry 1nyl
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Microlytics , MCSG1 C2 opt: 100mM BisTris pH 6.5, 200mM Lithium-sulphate, 23% PEG 3350; PsaeA.18222.a.B1.PW37623 at 20 mg/ml + 2.5mM AMPPNP and MgCl2; cryo: 20% EG + AMPPNP/Gln in two steps; tray 262504b8, puck bfw9-7
Crystal Properties Matthews coefficient Solvent content 2.99 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.01 α = 90 b = 56.02 β = 99.41 c = 127.14 γ = 90
Symmetry Space Group P 1 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 RAYONIX MX-225 2015-03-26 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) 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 1.9 50 99.8 0.095 11.71 5 119957 119747
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 1.9 1.95 99.6 0.461 3.31 5
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 1nyl 1.9 41.809 1.34 119727 1999 99.84 0.1883 0.1876 0.1896 0.2282 0.2294 Random selection 22.6515
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 13.466 f_angle_d 1.006 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8607 Nucleic Acid Atoms Solvent Atoms 1522 Heterogen Atoms 22
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing BALBES phasing RESOLVE model building Coot model building PHENIX phasing PHENIX refinement