☰ Navigation Tabs
Crystal structure of Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan-tRNA ligase)(TrpRS) (tm0492) from THERMOTOGA MARITIMA at 2.50 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YI8 1yi8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 12.5% PEG-3000, 0.25M MgCl2, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.37 63.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.89 α = 90 b = 152.73 β = 90 c = 53.07 γ = 90
Symmetry Space Group C 2 2 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 315 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 ALS 8.2.2
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 2.5 29.64 91.4 0.078 8.82 1.93 17636 49.406
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 2.5 2.59 97.9 82.4 0.47 2.1 1.86
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 (All) 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 1yi8B 2.5 29.64 17623 894 99.28 0.197 0.19724 0.194 0.196 0.256 0.2506 RANDOM 35.567
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] 2.09 -1.52 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.224 r_dihedral_angle_4_deg 14.102 r_dihedral_angle_3_deg 11.769 r_scangle_it 6.681 r_scbond_it 4.903 r_dihedral_angle_1_deg 3.256 r_mcangle_it 2.751 r_mcbond_it 1.704 r_angle_refined_deg 1.603 r_angle_other_deg 1.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.224 r_dihedral_angle_4_deg 14.102 r_dihedral_angle_3_deg 11.769 r_scangle_it 6.681 r_scbond_it 4.903 r_dihedral_angle_1_deg 3.256 r_mcangle_it 2.751 r_mcbond_it 1.704 r_angle_refined_deg 1.603 r_angle_other_deg 1.012 r_mcbond_other 0.328 r_symmetry_vdw_refined 0.282 r_nbd_refined 0.226 r_nbd_other 0.191 r_nbtor_refined 0.184 r_symmetry_vdw_other 0.17 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.099 r_nbtor_other 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2547 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing