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Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with a glutamyl-AMP analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O5R PDB ENTRY 2O5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.25mM MgCl2, 4.5mM 2-mercaptoethanol, 22.5mM NaCl, 3% D-sorbitol, 45mM HEPES-NaOH buffer (pH 7.5), 3.6% ethylene glycol, 6.75% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.624 α = 90 b = 207.317 β = 90 c = 39.495 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210r mirrors 2008-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 50 95.7 0.095 17.9 6.4 37578 -3 16.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 72 0.402 2.2 4.8 2799
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 2O5R 2 39.5 37512 1866 95.5 0.186 0.186 0.1865 0.235 0.2346 RANDOM 30.5
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] 1.45 -9.77 8.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.8 c_scangle_it 4.76 c_scbond_it 3.34 c_mcangle_it 2.67 c_mcbond_it 1.97 c_angle_deg 1.2 c_improper_angle_d 0.81 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.8 c_scangle_it 4.76 c_scbond_it 3.34 c_mcangle_it 2.67 c_mcbond_it 1.97 c_angle_deg 1.2 c_improper_angle_d 0.81 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3855 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling