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Crystal Structure of Thioredoxin Wild Type 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, Ac2Cu 1mM, AcNa 15mM, HEPES 15 mM pH 6.9, pH 3.5, Counterdiffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.79 55.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.727 α = 90 b = 102.727 β = 90 c = 42.865 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 2006-03-28 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 2.6 51.36 99.8 0.0787 9.08 7.28 8147 8147 51.288
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 2.6 2.65 100 0.3161 2.63 7.28 464
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2TRX 2.6 44.5 8147 8077 370 99.18 0.222 0.222 0.219 0.284 RANDOM 43.014
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] -0.48 -0.24 -0.48 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.224 r_dihedral_angle_3_deg 16.628 r_dihedral_angle_4_deg 15.798 r_dihedral_angle_1_deg 6.349 r_mcangle_it 1.954 r_scangle_it 1.636 r_angle_refined_deg 1.427 r_mcbond_it 1.193 r_scbond_it 1.142 r_symmetry_hbond_refined 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.224 r_dihedral_angle_3_deg 16.628 r_dihedral_angle_4_deg 15.798 r_dihedral_angle_1_deg 6.349 r_mcangle_it 1.954 r_scangle_it 1.636 r_angle_refined_deg 1.427 r_mcbond_it 1.193 r_scbond_it 1.142 r_symmetry_hbond_refined 0.366 r_nbtor_refined 0.309 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.21 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction SAINT data scaling SADABS data scaling XPREP data reduction AMoRE phasing Coot model building MolProbity model building