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Crystal Structure of Thioredoxin Mutant D2E 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, AcNa 15 mM pH3.5, Ac2Cu 1 mM, Counter-diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.497 α = 90 b = 103.497 β = 90 c = 41.78 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 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 2.4 44.82 99.7 0.0242 32.58 10.9 10198 10198 49.79
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 2.4 2.45 97.9 0.2876 4.36 5.89 605
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 2.4 44.82 10198 10162 1014 99.471 0.206 0.206 0.2007 0.2018 0.2575 0.2565 Random 20.845
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] -2.785 -1.392 -2.785 4.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.013 r_dihedral_angle_3_deg 16.221 r_dihedral_angle_1_deg 6.908 r_dihedral_angle_4_deg 4.366 r_mcangle_it 1.93 r_scangle_it 1.789 r_angle_refined_deg 1.597 r_mcbond_it 1.27 r_scbond_it 1.226 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.013 r_dihedral_angle_3_deg 16.221 r_dihedral_angle_1_deg 6.908 r_dihedral_angle_4_deg 4.366 r_mcangle_it 1.93 r_scangle_it 1.789 r_angle_refined_deg 1.597 r_mcbond_it 1.27 r_scbond_it 1.226 r_nbtor_refined 0.304 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.204 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.094 r_bond_refined_d 0.029 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 60 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