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Structure of human tryptophanyl-tRNA synthetase in complex with tRNA(Trp)
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 7 277 ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.8 74.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.2 α = 90 b = 133.2 β = 90 c = 138.3 γ = 90
Symmetry Space Group P 43 2 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 MARRESEARCH 2005-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.0000 BSRF 3W1A
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 3.1 50 100 0.128 6.7 5.9 23201 23201 61.5
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) 3.1 3.29 100 0.568 3 6 2246
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-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 3.1 47.97 23169 1167 99.8 0.23 0.2244 0.27 0.2624 RANDOM 70.5
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] 3.5 8.13 -11.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.1 c_scangle_it 13.05 c_scbond_it 9.42 c_mcangle_it 6.61 c_mcbond_it 4.09 c_angle_deg 1.2 c_improper_angle_d 1.15 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.1 c_scangle_it 13.05 c_scbond_it 9.42 c_mcangle_it 6.61 c_mcbond_it 4.09 c_angle_deg 1.2 c_improper_angle_d 1.15 c_bond_d 0.008 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 3015 Nucleic Acid Atoms 1541 Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose CNS refinement XDS data reduction HKL-2000 data scaling CNS phasing