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Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 45% MPD, 5MM CUPRIC ACETATE, 0.1M SODIUM ACETATE, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.047 α = 90 b = 51.042 β = 90.43 c = 88.973 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 RIGAKU RAXIS VII 2005-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW
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 2.5 33.54 88.6 0.093 0.093 3.3 15797 15051
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 2.5 2.59 70 0.357 0.357 1.7
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 2TRX 2.5 33.54 14301 750 95.3 0.236 0.232 0.2309 0.311 0.3089 RANDOM 28.98
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] 0.12 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.221 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 17.685 r_dihedral_angle_1_deg 5.824 r_scangle_it 2.187 r_angle_refined_deg 1.447 r_scbond_it 1.339 r_mcangle_it 0.996 r_mcbond_it 0.566 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.221 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 17.685 r_dihedral_angle_1_deg 5.824 r_scangle_it 2.187 r_angle_refined_deg 1.447 r_scbond_it 1.339 r_mcangle_it 0.996 r_mcbond_it 0.566 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.239 r_metal_ion_refined 0.223 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3256 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 4
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling