☰ Navigation Tabs
Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG 1000, MES (2-(N-morpholino)ethanesulfonic acid) pH 6.3, bicine (N,N-bis(2-hydroxyethyl)glycine) pH 9.0, MnCl2, MgCl2, sodium cyanide and L-Trp
Crystal Properties Matthews coefficient Solvent content 2.28 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.095 α = 90 b = 117.752 β = 95.52 c = 138.819 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2011-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97828 ESRF BM14
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 1.7 117 98 0.055 13.4 3.7 268120
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 1.7 1.79 2.9
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 2NW8 1.7 89.78 254545 13541 97.94 0.1507 0.1488 0.1621 0.1851 0.1953 RANDOM 23.854
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.797 r_dihedral_angle_4_deg 20.531 r_dihedral_angle_3_deg 13.277 r_dihedral_angle_1_deg 5.248 r_angle_refined_deg 1.692 r_angle_other_deg 1.484 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.797 r_dihedral_angle_4_deg 20.531 r_dihedral_angle_3_deg 13.277 r_dihedral_angle_1_deg 5.248 r_angle_refined_deg 1.692 r_angle_other_deg 1.484 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18397 Nucleic Acid Atoms Solvent Atoms 1924 Heterogen Atoms 680
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing