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Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other LOW RESOLUTION MAD STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 RESERVOIR: 0.1 M SODIUM CITRATE BUFFER PH 5.5, PEG 4000 8% (W/V), 15% MPD (V/V), 0.1M KCL, 1MM MGCL2 DROPLET: 2 MICROL TYRRS 14 MG/ML IN 20 MM TRIS PH 7.4, 1MM TYROSINOL, 1MM ATP 0.5 MICROL RESERVOIR
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.502 α = 90 b = 107.3 β = 90 c = 148.89 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 CCD ADSC QUANTUM 210 MIRROR 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.2 87 100 0.09 2.2 4.5 52537 25.9
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 2.2 2.28 100 0.29 2.3 4.6
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT LOW RESOLUTION MAD STRUCTURE 2.2 29.83 52432 2641 99.9 0.216 0.216 0.248 RANDOM 39
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] -4.07 5.05 -0.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.5 c_scangle_it 3.48 c_scbond_it 2.38 c_mcangle_it 2.32 c_mcbond_it 1.44 c_angle_deg 1.1 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.5 c_scangle_it 3.48 c_scbond_it 2.38 c_mcangle_it 2.32 c_mcbond_it 1.44 c_angle_deg 1.1 c_improper_angle_d 0.71 c_bond_d 0.006 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 5169 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 24
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling AMoRE phasing