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Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y2Q PDB ENTRY 1Y2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 25% PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.02 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.652 α = 90 b = 67.363 β = 90 c = 98.588 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2005-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.6 25 97.8 0.08 14.75 3.6 8487 8487 63.8
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) 2.6 2.69 86.3 0.409 2.12 2.8 724
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 (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 1Y2Q 2.6 24.84 8432 8432 438 98.4 0.213 0.213 0.2136 0.295 0.2951 RANDOM 43.8
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] 4.47 -5.36 0.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 3.09 c_mcangle_it 2.19 c_scbond_it 1.96 c_angle_deg 1.4 c_mcbond_it 1.28 c_improper_angle_d 0.77 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 3.09 c_mcangle_it 2.19 c_scbond_it 1.96 c_angle_deg 1.4 c_mcbond_it 1.28 c_improper_angle_d 0.77 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_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 2280 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 58
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing