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Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HC7 PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.9 SEE REFERENCE 3, pH 7.90
Crystal Properties Matthews coefficient Solvent content 4.42 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.29 α = 90 b = 141.29 β = 90 c = 237.56 γ = 90
Symmetry Space Group P 43 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 100 IMAGE PLATE MARRESEARCH 1998-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID2 ESRF ID2
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 20 99.6 0.067 3.8 48648
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 3.08 100 0.269 2.7 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE) 3 20 48593 2452 99.8 0.221 0.221 0.254 0.2294 RANDOM
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] 0.421 0.421 -0.843
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 5.82 c_mcangle_it 3.78 c_scbond_it 3.5 c_mcbond_it 2.13 c_angle_deg 1.392 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 5.82 c_mcangle_it 3.78 c_scbond_it 3.5 c_mcbond_it 2.13 c_angle_deg 1.392 c_bond_d 0.007 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 c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7479 Nucleic Acid Atoms 1436 Solvent Atoms 24 Heterogen Atoms 88
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling AMoRE phasing