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Glutamine synthetase from Methanothermococcus thermolithotrophicus with TbXo4 at a resolution of 1.65 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LNN Glutamine synthetase from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Crystallization was performed in an anoxic tent (with a gas phase of 95% N2/5% H2) on a 96-well two-drop MRC crystallization plate in polystyrene (Molecular Dimensions, Suffolk, UK). The sitting drops contained a mix of 0.7 ml of the glutamine synthetase at 15 mg/ml with 10 mM TbXo4 and 0.7 ml of precipitant solution (35 % Pentaerythritol ethoxylate (15/4 EO/OH), 200 mM Ammonium sulphate, 100 mM HEPES pH 7.5).
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.434 α = 90 b = 228.448 β = 90 c = 204.803 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2016-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.65 49.78 98.9 0.063 0.074 0.039 0.999 11.9 6.9 361584
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 97.9 0.918 1.081 0.566 0.782 1.6 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.65 49.78 1.33 361148 17860 98.72 0.1641 0.163 0.1679 0.185 0.1892 33.52
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 21.678 f_angle_d 1.485 f_chiral_restr 0.117 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21204 Nucleic Acid Atoms Solvent Atoms 2932 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing