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Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3N PDB ENTRY 1H3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 5MG/ML LEUCYL-TRNA SYNTHETASE MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5 MM L-LEUCINE 15MM MGCL2 50MM MES PH6.5 0.8M AMMONIUM SULPHATE AGAINST RESERVOIR CONTAINING 1.5M AMMONIUM SULPHATE AND 0.1M MES PH6.5, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.9 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.869 α = 90 b = 125.578 β = 118.44 c = 172.979 γ = 90
Symmetry Space Group C 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 ADSC CCD TOROIDAL MIRROR 2003-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.3 25 98.7 0.1 12.1 4.4 57205 110.1
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 3.3 4 98.4 0.22 7.33 4.4
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 1H3N 3.3 24.45 57205 2289 99.1 0.243 0.243 0.2253 0.282 0.2548 RANDOM 85.5
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] 29.68 29.38 -18.97 -10.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_scangle_it 4.85 c_scbond_it 3.07 c_mcangle_it 2.49 c_mcbond_it 1.4 c_improper_angle_d 1.28 c_angle_deg 1.2 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_scangle_it 4.85 c_scbond_it 3.07 c_mcangle_it 2.49 c_mcbond_it 1.4 c_improper_angle_d 1.28 c_angle_deg 1.2 c_bond_d 0.009 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 14244 Nucleic Acid Atoms 3354 Solvent Atoms Heterogen Atoms 99
Software Software Software Name Purpose CNS refinement XDS data reduction XSCALE data scaling MOLREP phasing