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Crystal Structure of Thioredoxin Mutant D13E in Hexagonal (p61) Space Group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX pdb entry 2TRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 3.5 277 60% (v/v) MPD, Hepes 15 mM pH 7.0, Ac2Cu 1mM, pH 3.5, Counter-diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.081 α = 90 b = 103.081 β = 90 c = 42.588 γ = 120
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 BRUKER SMART 6000 Montel Optics 2005-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 51.54 99.9 0.0258 23.38 1.92 13343 13343 38.183
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.25 100 0.1934 4.16 1.7 856
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2TRX 2.2 51.54 13343 12846 1273 96.297 0.233 0.233 0.2269 0.2275 0.2935 0.2848 Random 43.267
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] -4.208 -2.104 -4.208 6.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 23.872 r_dihedral_angle_3_deg 15.705 r_dihedral_angle_1_deg 5.775 r_mcangle_it 1.869 r_scangle_it 1.532 r_angle_refined_deg 1.229 r_mcbond_it 1.179 r_scbond_it 1.004 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 23.872 r_dihedral_angle_3_deg 15.705 r_dihedral_angle_1_deg 5.775 r_mcangle_it 1.869 r_scangle_it 1.532 r_angle_refined_deg 1.229 r_mcbond_it 1.179 r_scbond_it 1.004 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1630 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 16
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction SADABS data scaling XPREP data reduction Coot model building MolProbity model building