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Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococcus janaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Thermus Thermophilus Proline tRNA Synthetase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 Sodium Acetate, Ammonium Sulfate, PEG 4000, beta-Mercaptoethanol, Tris, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.46 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.94 α = 90 b = 104.845 β = 93.63 c = 91.748 γ = 90
Symmetry Space Group P 1 21 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 QUANTUM 4 2000-05-29 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 4 2000-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.943 CHESS F1 2 SYNCHROTRON ALS BEAMLINE 5.0.1 1.100 ALS 5.0.1
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 1,2 3.2 20 86.9 0.102 7.9 2.5 34834 30271 -3
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) 3.2 3.31 80.3 0.38 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Thermus Thermophilus Proline tRNA Synthetase 3.2 20 34036 29611 2954 87 0.2311 0.2311 0.231 0.2231 0.301 0.2836 RANDOM 65.4
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] -12.93 10.96 -25.61 38.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 11.38 c_mcangle_it 8.71 c_scbond_it 7.51 c_mcbond_it 5.32 c_angle_deg 1.4 c_improper_angle_d 0.86 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15088 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement