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Tryptophanyl-tRNA synthetase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DR2 PDB ENTRY 2dr2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 0.2 M Sodium Malonate, 20% PEG 3350, 1mM TCEP, pH 7.0, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.294 α = 95.29 b = 51.426 β = 100.14 c = 89.97 γ = 106.05
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 2008-10-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 30.76 97.1 0.077 9.2 3.07 20576 76
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 2.8 2.9 95.7 0.324 2.6 3.08 2053
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 2dr2 2.8 30.76 20555 1065 96.95 0.244 0.241 0.2379 0.301 0.2873 RANDOM 5.391
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] -0.33 1.18 0.91 1.21 1.93 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.38 r_dihedral_angle_4_deg 18.535 r_dihedral_angle_3_deg 18.491 r_dihedral_angle_1_deg 7.046 r_scangle_it 1.547 r_angle_refined_deg 1.238 r_scbond_it 0.933 r_angle_other_deg 0.922 r_mcangle_it 0.686 r_mcbond_it 0.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.38 r_dihedral_angle_4_deg 18.535 r_dihedral_angle_3_deg 18.491 r_dihedral_angle_1_deg 7.046 r_scangle_it 1.547 r_angle_refined_deg 1.238 r_scbond_it 0.933 r_angle_other_deg 0.922 r_mcangle_it 0.686 r_mcbond_it 0.367 r_chiral_restr 0.083 r_mcbond_other 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5199 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction BALBES phasing