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Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp
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 5.125214 76.000999
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 252.655 α = 90 b = 252.655 β = 90 c = 111.805 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 2.8 50 99.6 0.086 16.9 6.7 99766
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) 2.8 2.9 98.7 0.363 5.1 9805
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 2.8 47.75 94506 5014 99.41 0.21769 0.21617 0.2133 0.24665 0.2145 RANDOM 67.191
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] -2.44 -1.22 -2.44 3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.726 r_dihedral_angle_3_deg 15.795 r_dihedral_angle_4_deg 14.465 r_scangle_it 5.656 r_dihedral_angle_1_deg 4.767 r_rigid_bond_restr 4.136 r_scbond_it 4.106 r_mcangle_it 3.214 r_mcbond_it 2.749 r_sphericity_bonded 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.726 r_dihedral_angle_3_deg 15.795 r_dihedral_angle_4_deg 14.465 r_scangle_it 5.656 r_dihedral_angle_1_deg 4.767 r_rigid_bond_restr 4.136 r_scbond_it 4.106 r_mcangle_it 3.214 r_mcbond_it 2.749 r_sphericity_bonded 1.382 r_sphericity_free 1.184 r_angle_refined_deg 0.943 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 13104 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 115
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