☰ Navigation Tabs
Structure of Trichomonas vaginalis thioredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TIR PDB model 2TIR manipulated with MODELLER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 293 PEG4000, ammonium sulfate, sodium acetate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.231686
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.882 α = 106.2 b = 33.923 β = 109.02 c = 50.497 γ = 91.68
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 4 2002-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 32.29 90.47 0.038 0.038 14.3 1.88 14430 14428 -3 -3 16.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 76.6 0.074 0.074 9.2 1.79 1234
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB model 2TIR manipulated with MODELLER 1.9 32.29 13709 13709 719 90.47 0.14728 0.14728 0.1447 0.1589 0.19685 RANDOM 7.857
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] 0.47 -0.37 -0.83 -0.17 0.01 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.247 r_dihedral_angle_4_deg 15.307 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_1_deg 4.781 r_scangle_it 2.175 r_scbond_it 1.697 r_angle_refined_deg 1.148 r_mcangle_it 1.107 r_mcbond_it 0.979 r_angle_other_deg 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.247 r_dihedral_angle_4_deg 15.307 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_1_deg 4.781 r_scangle_it 2.175 r_scbond_it 1.697 r_angle_refined_deg 1.148 r_mcangle_it 1.107 r_mcbond_it 0.979 r_angle_other_deg 0.773 r_symmetry_vdw_other 0.228 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.175 r_mcbond_other 0.173 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.153 r_nbtor_other 0.079 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1712 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing