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Tryptophanyl-tRNA synthetase from Giardia lamblia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IP1 PDB entry 2IP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.2 298 2.7 M (NH4)2SO4, 0.1 M Citric acid pH 5.2, 5mM DTT, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.33 63.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.714 α = 90 b = 140.147 β = 90 c = 90.352 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97945 SSRL BL9-1
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 2.09 40 97.3 0.089 20.921 6.9 77780
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 2.09 2.18 82 0.61 5.1 6455
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2IP1 2.09 40 77712 3910 96.71 0.2 0.199 0.2117 0.234 RANDOM 28.296
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] 3.84 -2.65 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.307 r_dihedral_angle_4_deg 17.34 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_1_deg 5.532 r_scangle_it 1.973 r_scbond_it 1.171 r_angle_refined_deg 1.003 r_mcangle_it 0.853 r_angle_other_deg 0.788 r_mcbond_it 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.307 r_dihedral_angle_4_deg 17.34 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_1_deg 5.532 r_scangle_it 1.973 r_scbond_it 1.171 r_angle_refined_deg 1.003 r_mcangle_it 0.853 r_angle_other_deg 0.788 r_mcbond_it 0.45 r_mcbond_other 0.069 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6371 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection