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Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with TrpAMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KT0 PDB ENTRY 3KT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 0.1M HEPES, 2.2M (NH4)2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.056929 75.676941
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 251.759 α = 90 b = 251.759 β = 90 c = 111.102 γ = 120
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 210r 2008-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 50 96.3 0.056 22.5 4.5 118348
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 83.4 0.344 2.3 10202
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 3KT0 2.6 48.94 112240 5918 96.08 0.21535 0.21421 0.2121 0.23672 0.2121 RANDOM 53.4
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] -2.08 -1.04 -2.08 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.779 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_4_deg 14.477 r_dihedral_angle_1_deg 5.127 r_scangle_it 4.919 r_rigid_bond_restr 4.151 r_scbond_it 3.888 r_mcangle_it 2.938 r_mcbond_it 2.342 r_sphericity_bonded 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.779 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_4_deg 14.477 r_dihedral_angle_1_deg 5.127 r_scangle_it 4.919 r_rigid_bond_restr 4.151 r_scbond_it 3.888 r_mcangle_it 2.938 r_mcbond_it 2.342 r_sphericity_bonded 1.522 r_angle_refined_deg 1.004 r_sphericity_free 0.669 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.197 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.093 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13105 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 213
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 PHASER phasing