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Structual basis of iodo-tyrosine recognition by engineered archeal tyrosyl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZH0 PDB ENTRY 1ZH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 24-28% PEG300, 5-8% PEG8000, 10% Glycerol, 0.1M TRIS, PH8.5, VAPOR DIFFUSION, TEMPERATURE 293K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.201 α = 90 b = 102.201 β = 90 c = 71.904 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 CCD ADSC QUANTUM 210 MONOCHROMATOR 2006-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 50 99.9 0.064 0.064 43.41 13.7 42504 -3 26.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 99.9 0.734 0.734 2.75 11.9
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 1ZH0 1.7 41.65 42370 4273 99.8 0.193 0.193 0.1916 0.22 0.2202 RANDOM 33
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] 3.88 3.88 -7.76
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 6.42 c_scbond_it 4.55 c_mcangle_it 3.18 c_mcbond_it 2.52 c_angle_deg 1.5 c_improper_angle_d 0.91 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 6.42 c_scbond_it 4.55 c_mcangle_it 3.18 c_mcbond_it 2.52 c_angle_deg 1.5 c_improper_angle_d 0.91 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 2474 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 14
Software Software Software Name Purpose MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling