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Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5T PDB ENTRY 1O5T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1M MES buffer, 0.05M CsCl, 30% v/v Jeffamine M-600 reagent, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.912 α = 90 b = 55.912 β = 90 c = 313.784 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 4r 2006-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.1 50 96.6 0.102 7.2 9.1 29469
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) 2.1 2.18 98.5 0.586 9.5 2911
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 1O5T 2.1 33.45 29427 1471 96.83 0.208 0.207 0.2102 0.238 0.2202 RANDOM 37.426
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] 1.88 1.88 -3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.777 r_dihedral_angle_3_deg 14.258 r_dihedral_angle_4_deg 12.437 r_sphericity_free 10.112 r_dihedral_angle_1_deg 5.283 r_scangle_it 3.948 r_scbond_it 2.486 r_mcangle_it 1.95 r_rigid_bond_restr 1.913 r_mcbond_it 1.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.777 r_dihedral_angle_3_deg 14.258 r_dihedral_angle_4_deg 12.437 r_sphericity_free 10.112 r_dihedral_angle_1_deg 5.283 r_scangle_it 3.948 r_scbond_it 2.486 r_mcangle_it 1.95 r_rigid_bond_restr 1.913 r_mcbond_it 1.456 r_sphericity_bonded 1.157 r_angle_refined_deg 1.075 r_nbtor_refined 0.307 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3025 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing